Hmm, it seems like the ticks are not integrated into protrusions in PolarAxis, so this might be an issue.
The quick fix is to set polar_axis.thetaticklabelsize and polar_axis.rticklabelsize to 0. That should get you most of the way there.
So the alignmode etc can’t actually help, since they don’t know about the ticks.
Here’s an MWE stepping through what I did:
θ = range(-π, stop=π, length=100)
r = 0.1 .+ rand(100)
f, a, p = lines(r, θ; axis = (; type = PolarAxis))
b = Box(f[1, 1]; color = (:red, 0.3))
translate!(b, 0, 0, 10000) # get the box on top of the polar axis
f
hidedecorations!(a)
(this is still bad)
a.thetaticklabelsize[] = 0
a.rticklabelsize[] = 0
It’s still not 100% tight, but at least mostly there. It would be great if you could open an issue on the Makie repo with this info!