I know mods would probably already reject a run if it was done in the In Dev version for multiple reasons including the fact that there are a lot less public players, but just to make sure there are no loopholes you mods should put it in the rules so that nobody does it on accident or something like that.
Well, since the in dev version is a completely different place on Roblox, any runs from there will be rejected by default. I'm pretty sure the run having to be from the game you submit it to is in the site rules.
Well some Roblox games game moderators make a separate experience that you are required to use for speedrunning on their leaderboards cough cough TP.
Actually, after some further thought, it depends on if the advantage from In Dev is noticeable or not. At times when In Dev is pretty much the same as normal Flee the Facility runs from there will probably be accepted. However, if playing on In Dev offers any noticeable advantage, the run will be rejected.
In other words, runs from the In Dev version will only be accepted if the round doesn't include any gameplay altering features not already present in the standard game of Flee the Facility.