I shall preface this that none of this is meant to be in any way accusatory or harshly worded or over critical, just stating what I can and cannot do when trying to interact with the program. Tone is always hard to convey, I could pepper this with smileys but they'd feel out of place.
Thanks for the explanation about how to apply TR moves. Perhaps then the error should be "TR not selected" rather than "illegal move"? I can understand not wanting the app to automatically toggle that state when you add/remove the move, as that may not be an intended consequence. I'd installed ALM, but it's not as A as I'd expected; that also helped fix it and I shall know how and when to trigger in future edits.
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I don't have any pokémon in boxes, I'm not using a dumped file from a Switch, so I have no idea what options might be available from left or right clicking on anything in those areas. I had no idea what modifier keys may exist for interacting with them, as I could see no examples in the app to show me. (I have now found that list, will return to that lower down) As the context menu in the Encounter database consists solely of View, the same applies - no idea what if any modifier keys may be expected to perform any given task, nor any idea what those tasks might be. But if I did have saved Switch data, I would be able to see a change if I right-clicked and picked View, as the slot data wouldn't be obscured by the menu I was using, whereas I had no feedback that doing this in the Encounter database made anything happen.
I natively use a Mac, which is why I have taken a while to get around to using PKHeX directly. On a Mac ctrl-click is interpreted as right-clicking, and there's no easy way to disable this; there's not really a hard way to either, Mac software is designed to avoid having to do so. Through the set-up I'm using (Mac controlling a Windows PC running PKHeX), ctrl-click accomplishes nothing at all - it doesn't emulate a right-click, and it doesn't select a slot for viewing as I believe you're suggesting. I see there's quite a few ctrl+click options, all of these are also unavailable. Obviously I'm an edge case and I recognise that, aside from guaranteeing Xor1 shiny selection I don't think there's anything that I can't access in another way though, which is great and shows the amount of thought that has been put into this interface.
Regarding the shortcut list, having it as a sub-menu in the About section means you can't keep the list open for reference when using the app. My short-term memory is absolutely terrible thanks to ADHD, I will eventually remember things after multiple repetitions but without being able to have something to refer to my chances of learning these drop considerably. Could it possibly be set so we can keep it open, like the encounter list? Perhaps also wordwrap could be enabled or the size of the windows expanded, as the text flows outside the current area.
(I am very glad this board caches entered messages. This took a while to get down and I almost lost it.)