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.
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.
@GanhadorDoGrau, this forum was started by a runner named Skittles, who has since deleted his account. He was requesting us mods to ban the in dev version of FtF I think.