Very strange! I'd like to say it's related to the other seeding issue which was fixed for Beta 8, the one with the schematics etc., but accessibility to branches should be unaffected by that (or anything else that happens during a run, to be honest) since it's all predetermined when you first start the seed.
According to 7.1 data/behavior, the seed FactoryActuatorExpander places Extension on -6, regardless of whether or not you've been through Waste, so that first use of the seed, randomly, is what's different from what it is when seeded manually.
Now that I mention it, there are some cases I need to look into because manually seeding a run as opposed to getting the same seed randomly can have some effects on the content! This is normal/intended, though I'm surprised that the changes are large enough to affect the actual branch depths.
Actually, as a quick test I could turn off the manual seed designation and let the game think the seed I've manually assigned was a random choice, which maybe could end up putting Extension on -4...
...and unfortunately that does not seem to change the results, it's still on -6!
So clearly it should be on -6, and now I'm really curious how you got to it on -4, but I guess we can't investigate further without a save from that run :/
Still not yet sure whether this is a bug or not. Certainly unintended behavior, but it could be caused by something intended which overrides that need, I dunno. I can't think of anything that could cause this since the map depths are determined before anything else, and cannot be changed. Hm.
Interesting to finally have some info coming in from seeded runs, in any case. We have other people referring to old seeds and using those to reach confirmed maps/events, though I don't recall any instances like this.
Going to just have to wait on this on to see if any more info pops up. Sorry for the troubles there xD. If we could have save data from the first run that'd be great, but I guess that's long gone now...