I had the same experience with this game playing it casually; everything except the folio bruti can be completed. That is because the 3 monsters you mentioned cannot be encountered in the game.
I think that is fine. Some additional mouse buttons can be set in the in-game keybinding options if you enable Raw mouse input in Kentie's DeusExe launcher options, then once you know the name for that mouse button (something like Unknown05 for example) you can set it in the user.ini file.
Sorry for the late reply. I don't check these forums all that often.
About the skip: there is a video on it which shows how it works with the keyboard inputs (now in the guides section here). The movement isn't too hard, but during a run it will be completely blind. Just give it a little bit of practice (without triggering the cutscene, first with eyes open then with eyes closed and record it to see later what you did) and it shouldn't be too difficult.
Normally runs are timed from the beginning of gaining control of Jensen (or gaining control of a conversation) until losing control of Jensen or control of the final conversation. In your submitted runs the timer start/stop times are fine.
For absolute zero I agree that a category should be added on the leaderboards. The rules for the DXHR absolute zero state "No items/augmentations/takedowns/alarms" (no alarms part basically means 100% stealth), with any difficulty. Originally it was on the hardest difficulty but not anymore since some inevitable fights are shortened tremendously on easy difficulty. For DXMD it's tricky for the no augmentations part, since you start with many of them, to lose them later on. I'd say active augmentations that cost bioenergy should be banned from use, unless there is an obstacle that can't be overcome in any other way. Passive augmentations like the leg augmentations and Icarus landing are not so easy to ban like that. Exceptions to the rules can always be made if necessary.
Don't worry about the few seconds that are missing from the vod. I don't think glitchless will be very competitive, but there are good enough reasons to include it as a category. Foxiest has never been a separate category, except if you look at Absolute Zero, which qualifies as a low% category.
There are new (empty) splits now on the resources page, which hopefully aren't as confusing as the previous ones