There's a new update (tentatively v2.15) incoming to the game in the works that addresses the potential softlock from the Dylan FLST timeskip in the start of the game, but basically nerfs speedrunning. I quote Mike Lasch from the Discord:

"The way the skip works now takes you to Ch2, not Ch3, because we don't want players who work out FLST and Dylan's files early in Ch1 to miss Ch2 stuff. So it will add time, but it now makes sense story-wise and doesn't cause what appears to be a soft-lock for folks playing through the first time"

I know we already use the earliest available version (v1.04) for speedrunning, but are we keen on making new categories for various versions (and reclassify the old records under v1.04)? Personally, anything goes!

Update to the update: HUZZAH! Got some cool news to share. In the grand scheme of things it's not that large but hopefully there's no more need for the somewhat tedious process to get to v1.04 :D

Nice, that's good to hear, I'm currently downloading it myself to check but I'd be surprised if it didn't work fine. It makes sense to patch (and I'm surprised it wasn't done sooner but I expect it was harder to patch than the HAP skip).

I haven't been keeping up to date with development of the game, but if the update brings in more gameplay or variation maybe it could be a different category? Right now I think just keeping Any% (in this case, Any% HAP Skip/No HAP Skip) to whatever version is the fastest makes sense. I'd still like to see more people run All Cases if they want a fuller run experience. ;)

(For a good recent example of "whatever version is fastest": GTA San Andreas recently got a big skip for Any%, but only if you play on the pretty bad Windows Store version, but it's the fastest for Any%.)