I think you might be using your macro incorrectly.
It sounds like what you're doing is having a macro to use both embraces, another macro to use both #2 skills, another macro to use both #3 skills, etc.. This will lead to confusion as the icons won't match and skill queuing issues.
What you want to do is have a macro to switch the skills themselves when you summon, therefore the macro itself only runs on Summon.
For example this is my Eos Summon:
/merror off
/micon Summon
/pac "Obey" <me>
/ac Summon <wait.4>
/crosshotbar pet "Embrace" "Eos" 1 RA2
/pac "Obey" <me>
That is my Selene Summon
/merror off
/micon "Summon II"
/pac "Sic" <me>
/ac "Summon II" <wait.4>
/crosshotbar pet "Embrace" "Selene" 1 RA2
/pac "Sic" <me>
In both macros, I allocate the correct Embrace skill to the same spot on my hotbar. I also use the macro to automatically put Eos on Obey, as she is best used that way, and Selene on Sic, because I only use her for easy content where I want the dps boost as often as possible. If I need her on Obey (rarely), I have Obey & Sic allocated on my hotbars to switch.
Yes doing it this way means you actually need to pick a hotbar spot (and if you change it, you need to change your macro) but it's a much clearer way to do this as the skill itself isn't macroed so you'll see your cooldowns and icons properly.
Note: /crosshotbar is for people using the cross hotbar (controller set up)
For keyboard hotbars it's
Eos summon:
/hotbar pet "Embrace" "Eos" 1 2
Selene summon:
/hotbar pet "Embrace" "Selene" 1 2
1 being the hotbar #
2 being the slot within that hotbar
So that example is swapping slot 2 on hotbar 1
I didn't do it for the other 3 skills because I have them placed in different locations based on category (Selene's Fey Caress is right next to my Esuna, for example. Whereas I have Fey Covenant next to my Sacred Soil), however you certainly could do it for all of the pet skills. This would allow you to use only 4 slots for actual pet skills instead of 8 and have no macro icon/queuing/cooldown-display issues because it's done during the summon.
Other macros I use:
Whispering Dawn + Rouse:
/macroicon "Whispering Dawn" pet Eos
/ac "Rouse"
/pac "Whispering Dawn"
Sacred Soil auto targeting
/merror off
/ac "Sacred Soil" <t>
/ac "Sacred Soil" <me>
/macroicon "Sacred Soil"
Shadow Flare auto targeting
/merror off
/ac "Shadow Flare" <t>
/ac "Shadow Flare"
/macroicon "Shadow Flare"
The auto targeting macros are mostly because I play on controller and the time lost from skill queuing is far less than the time I'd lose if I were to manually target using the controller.
and of course a Rez macro
All in all I have 3 cross hotbars used (48 slots!), including limit break and 3 items. (Yeah, scholar is crazy. I don't have anywhere near this much on white mage or any other job really)
I realize you are on a keyboard/mouse and not controller, but you can still draw inspiration from controller set ups:
https://supernova-squirrel.herokuapp...IddF98887Z40GD
(if link doesn't work)
https://supernova-squirrel.herokuapp.com/ -> Browse Kits -> filter on scholar -> Squintina's
Some people who are on mouse/keyboard also have non-button hotbars that they click on for things that are used less frequently.
For example you don't need to put Rez on a button, just put it on a non-button hotbar (with a bigger display) and click when needed. Same with Limit Break, Protect, Dissipation.
Hotbar 1 = normal buttons
Hotbar 2 = Ctrl + buttons
Hotbar 3 = Alt + buttons (though usually ends up being clicked)
Hotbar 4 (gigantic) = click only
That was my MMO mouse setup (12 side buttons) when I was considering switching back to KB/mouse (but then decided controller felt better on scholar). I was going to enhance my summon macro to change the skills on hotbar 4. It's by no means perfect as I only used it briefly before going back to controller, but it illustrates my point about click-only hotbars.