The "issue" as I understand it stems from the fact that XIV doesn't expect or really want you to have more than the one character per server.
A majority of the underlying systems seem to be built with the expectation that alts are not something people do.
Seding mail? Not to your alts, unless you managed to bug them onto your friendslist or something you need a middle man.
(Past) Seasonal events? Do these on each character or sink money into replica items from the shop.
Sharing the one private house you can get per world per account? Nope.
A good portion of the cash shop items? Single-character with no option to pay more for an account-wide option.
Community contest rewards like the Cloud hair? Single. Character. Go win more contests on your alts.
Creating an alt character on a congested world you already have characters on? Wait for the lock to lift like everyone else. We can't have you bypass the lock if you already have a character on that world. You might break the time-space continuum and log both in simultaneously or something.

The way the MSQ-lock interacts with alts (which is to say it doesn't) is just another point in that list.
There simply is no consideration of "this is an alt, different rules apply here" - it's a concept that doesn't exist as far as the game is concerned.

Their "solution" to this is Fantasias and since those are printing money they really have no incentive to make this game any less alt-unfriendly.
It's like they looked at their competitors, saw them charging money for character renames and race changes and figured they'd copy that, without considering that those competitors encourage alts so nobody has to race-change their one character just to look at something different every now and then.

Short of putting up with the limitations or dropping the prospect of alts there's really no solution to be offered. The problem is baked into the game if you will.