Looks like that check got added in 3.5 (3523). So, going back to 3.5 (3522) or before would also work.
Glyphs implementation likely just needs to adjust the calculation for what might be considered too far as reasonable based on UPM and consider changing to a warning. I haven’t seen the case that caused the check to get added. I expect it should be a simple fix.
The check seems to be a bit too harsh. But I just did some more test. The limit is not related to the UPM but about the absolute values. There is a limit what the format can store. But that is seldom a problem. Some apps (Adobe) cause problems much earlier. e.g. a CFF based font is not allowing coordinates bigger than ~10000 units.
this is a screenshot from Indesign. Top is TTF below is CFF.