To be frank, personally I doubt that there are technical issues at all to begin with. I cannot imagine people capable of programing such a game to not know about the very basics of databases and their management, which is one of the most important parts of doing any program (game or otherwise). The excuse "technical limitations" is just that. Since no one can (legally) check the actual programing, no one can legally expose that they're just blatantly lying to avoid doing stuff that they don't feel like doing.
From a business perspective, businesses frequently do things that their clients don't want, in order to get more money. But "I want more money, so you have to pay for it too." sounds a lot worse than "I don't want to make you pay extra, but something outside of my control doesn't let me not take your money." does. Basically, Square Enix wants the game to have flawed systems in order to make paying extra to circumvent them more attractive. In this case, retainers are an example.
And the extra free slots?! Of course there's a point where players will just say "stop", especially in a subscription-based game. So they need to throw a bone here or there. Don't worry. They will just add a ton of new items to clog up your new inventory so you'll still want more.
This is a sad state, but honestly, I can understand it. There are few people like me that understand that businesses want to earn as much money and at as low a cost as possible. If they were honest, they would lose a lot of players feeling "hurt" in some way by that honesty. So they are just maiming those. In the end, the players still pay and play cause they enjoy the game overall.