Not a programming restriction - a narrative restriction. Basically, the writers had to decide whether they wanted to keep the writing so vague that you could do any content in any order and it would still make chronological sense. This would, for example, require characters to treat you as if meeting you for the first time EVERY TIME THEY MEET YOU, if they appear in multiple sidequests. Instead, the designers decided to write the content so that, whenever you actually do it, it is assumed to happen alongside the content that was added at the same time.
Whether you do Binding Coil or Stormblood first, Binding Coil is considered to come chronologically first. The silent assumption made when doing any old content is that it is assumed to take place in the past. This was first highlighted at the end of ARR, when Nanamo was seemingly dead - and yet you could still serve her a banquet during the ARR CUL quests. Even if you were only getting around to leveling CUL after completing the 2.55 MSQ, it's still understood that the events you're witnessing ACTUALLY take place around the same time as 2.0 MSQs.
So, Alisae isn't going back to wearing her old clothes when you run Coil. You're just witnessing events from the past, when she still dressed like her brother.
I presume you're speaking of Lakshmi's summoning at the leadership meeting? You're not giving her nearly enough credit. The text dialogue made it crystal clear that all involved - INCLUDING Lyse - expected the Qyalana might try something. They took proper precautions, confiscated their crystals, and so on and so forth. The Qyalana outmaneuvered them, but that doesn't indicate any sort of naivety or stupidity.
If you're arguing that the very concept of peace with the tempered is absurd, I disagree. Peace, at least a temporary peace, is VERY MUCH something that can be beneficial to the tempered (gives them time to consolidate their resources, and such), so it's entirely reasonable to assume that the Qyalana were genuine in their desire to have it. Tempered aren't mindless and endlessly predictable. They can strategize and prepare (heck, they wouldn't have pulled off the betrayal that they did without careful forethought). For the Alliance's part, having the Qyalana behave themselves for a while would have been very beneficial; the Garleans are a serious problem, and the more resources they could bring to bear against them, the better.
So, no, inviting the Qyalana was not naive or stupid. It was tactically desirable so as not to divide the Alliance's forces, and had a reasonable chance of being genuine since the Qyalana benefit as well (plus, refusing them would have given the Qyalana an excuse to step up hostilities). Measures were taken to guard against treachery, and even thought they turned out to be inadequate due to insufficient intelligence regarding enemy activities, they still imply the Alliance knew the risks of what they were dealing with.
Lyse is not my favorite character, to be sure, but holding this against her is quite unfair.



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