This sort of thing happens all the time. A band gets used to the timing and they do it because it sounds cool and feels right, time signature and tempo be damned.
I drum in a death metal band. We play live without a metronome but we record with one. Last week, we were going through a song and programming the click track. It’s a process of playing a riff, figuring out the comfortable tempo and time signature, setting it in Reaper, then playing along to it until there’s a change and doing it again. We hit this one transition that has these odd pauses. It’s very Suffocation, for any death metal fans out there. We always hold out one of them in a subtle way and discovered that we couldn’t find a way to program the section! The timing we were used to, especially me as the drummer, didn’t sync up with the a tempo that made sense, it wasn’t a countable number of beats. But we also did it evenly as a band for the past year, every time we played it, all together.
We wound up just deciding that we should play it to the click, speed up the pauses just a bit. It takes away a little personality but keeps the song tight.