Non-4/4 time signatures

How do you set up a “bar” to mean something other than “4 quarter notes”?

I just made some patterns in 5/8 in Polymetry mode and the transition between patterns is not in time.

if you change the track-length it shows how many bars it has

What exactly do you mean by transition between patterns? How do change between patterns?
There is this setting under Misc, the controls how much a pattern change is delayed … it should probably 1 Bar in you case.
Then a pattern change in Trackmode (STEP+TRACK) takes exactly 1 Bar

Couple of things to check - the run mode of each track needs to be set separately (under 2nd+track with track selected in track mode) - Free, Relatch and Trig being the modes. That caught me a few times. Relatch and Trig ensure the pattern starts from the top of its pattern, and can be used to synchronise it to other tracks that way in Seq mode … hope that helps?

In Polymetry, of course the lengths of the measures may differ between tracks (but you know that).

Settings menu allows for a default time signature … but sadly, 4/4 often asserts itself, even when no tracks are in 4/4. For instance, a current project of mine is in 6/4, with each quarter-note value playing at 102 when the Pyramid metronome is set at 68. One (Polyrhythmic) project I did had three different metric fields, all mathematically related, but the unheard common reference point, revealed in the displayed metronome value, was that quarter-note!! Can be a little perplexing.