Player with arthritis here, and some of your post makes me worry that you're a prime candidate for arthritis and/or carpal tunnel down the line. I don't want that to happen to anyone if it can be avoided!

I'm glad you're listening to your pain and adjusting the way you play, but I'd also recommend taking a 5 minute break every hour and periodically doing stretches. Trust me, you really don't want to get to the point where you develop a condition, and taking care of your hands will help you steer clear of that. So I really recommend being proactive now to prevent ending up in a place where pain is just part of your daily life. I am far from a medical expert, but I've found the stretches and advice in this video to be helpful for keeping my condition from worsening and reducing the frequency and intensity of my pain/discomfort: https://www.youtube.com/watch?v=EiRC80FJbHU&t=89s

As far as controllers and hotbars go, I have a few tricks that have helped me to be able to play comfortably, so maybe they'll help for you as well?

Macros
Macros are wildly misunderstood, which is understandable because the game doesn't explain them and that has lead to players unwittingly spreading a lot of misinformation about them. But if you understand macros, they can enhance your play while helping you take care of your hands. Here's a snippet from my thread on the benefits of macros:
Quote Originally Posted by LilimoLimomo View Post
You can reduce button bloat.
In my opinion, this is one of the biggest benefits of macros. When I started BLM in ARR, all the actions I needed to play could fit on a single crosshotbar. But as time has marched on, that is no longer the case. Especially if you're a controller player, you might struggle to find comfortable, convenient places to put all the different actions you use. You can manually swap through multiple crosshotbars or make use of features like the double-tap W-crossbars, but if those aren't quite cutting it, macros can make a huge difference.

For example, as of patch 6.48, there are 10 Dragoon combo skills — 7 for single-target, 3 for multi-target. That's a lot of button real estate! But if you'd prefer, you can use macros to make all of these skills pressable with only 4 controller buttons, without any damage loss. I made a short video demonstrating this: https://www.youtube.com/watch?v=YsZo2iWJDrs

What's actually happening here is that when you press a combo macro, it copies the buttons from a different crosshotbar onto you current crosshotbar. In this way, you can make macros so that when you press combo 1 it populates your crosshotbar with combo 2, then when you press combo 2 it populates your crosshotbar with combo 3, and so on.

It's worth pointing out that there is a cost to this specific method: the buttons that are being copied have to be stored in a different crosshotbar. Luckily, these can be literally any other crosshotbar; if you prefer, you can store your Dragoon crosshotbar configurations in your extra Dragoon crosshotbars, but you could also store them on any other class, including any of the 8 crosshotbars on non-combat classes like Botanist or pre-job classes like Gladiator. In this way you're unlikely to run out of space, but the initial setup and any modifications you make down the road will be that much more involved.

And you can do similar things with other classes as well. I cast Fire III with a macro that puts my fire spells front and center, and similarly when I cast Blizzard III my ice spells get put in those same spots. If you feel like you've got more buttons to press than you have UI to press them, then macros might be worth trying.
You can make single buttons that perform different actions depending on context.
You want a single button that casts Nascent Flash if you're targeting a party member, but if not casts Bloodwhetting? Macros can do that for you. Do you want a single button that does Heavy Swing if pressed within the GCD queue window, but performs Upheavel if not? Macros can do that for you.
You can automate single-weaves.
Generally speaking, it's not recommended to use the /wait command to chain several actions in a single macro. But if you have a situation where you want to do a single-weave after an instant-cast GCD, that can be done! For example, when my BLM casts Paradox(ice), that's when I always like to toss in a Sharpcast. With macros, I can automate that, which makes one less button to worry about.
You can automate chains of actions (though this comes with a meaningful caveat).
Because the /wait command only operates in multiples of 1 second, it's generally not recommend to use the /wait command to chain multiple actions; the reason is because to make this work in most cases, such macros will likely end up clipping the GCD, which results in action loss compared to pressing buttons manually. But that said, it's still worth talking about as a benefit. For people with certain disabilities or other needs, using such macros could possibly help them play the game more effectively and comfortably. That's why I'm listing this as a benefit, because for some players this will be.
Macros are code, so they can do other stuff, too.
I'm mainly putting this bullet point in as insurance, because I wouldn't be surprised if there are helpful things you can do with macros that I've never thought to do. If you have something combat-related that fits here, let me know! (I know there are plenty of great non-combat uses for macros, but I don't want to focus on those because I don't think anyone is genuinely saying not to use non-combat macros).
The full post, which includes follow-up posts that help design macros for players who replied, can be found here: https://forum.square-enix.com/ffxiv/...-or-Lost-Casts
Action Trays
Similar to what you mentioned, I use PC hotbars to create several "trays" of icon slots just underneath my crosshotbars. I use these to display the icons of the abilities that aren't otherwise displayed on my screen; for me, that means the abilities that are available when I hold R2+L2, as well as any abilities that are activated by macros without being the visible icon for a macro. I arrange the icons in consistent ways across my various jobs, such that there's a basic pattern of icons in certain places relating to certain buttons on my controller.
Now that I take breaks, stretch, and use macros and action trays, I've found that I can generally play FF14 both effectively and comfortably. I hope any of this helps in any way. Keep listening to your body, and if you need help making your own macros, let me know and I'd be happy to help!