Just bobbed a new stem on my bike and it is about 3mm taller than my old one leaving it just 1mm or so above the top of the steerer.
I added a spacer (on top of the stem/under the top cap) and preloaded the bearings, tightened up the stem as usual. I then removed the spacer under the top cap and put the top cap back on top of the stem and bolted up tight.

All will be well won’t it?

Yes, the top cap doesn’t do anything after the stem is tightened

100% sure?

yes, I run one of my bikes without a top cap at all

The only caveat I would add is that you carry a spacer on your first couple of rides. It’s not unheard of to need to make preload adjustments after a few miles, and you won’t be able to do it if the top-cap can’t compress the stem.

always have one in my bag for some reason anyhow cheers

Good Advise Three Fish!

Also, The cranks are looking good! 😀