Tool/proceedure to remove Shimano direct mount rim brake bearings (Ultegra in this case)

I would probably leave them alone unless you have a lot of confidence in yourself as a mechanic. Those are the brake posts that are pressed (not threaded) in at the factory, and serve as the brake mounting posts (since the frame doesn't have posts).

If you must disassemble these, you can watch a video of someone with very shaky hands pulling a slightly earlier generation of direct mount brake apart here:

Shimano Direct Mount Rear Brake Repair and Mods Tutorial Guide How To DIY

You'll have to make a couple of tools yourself, and if you're lucky, you won't scratch up the caliper or accidentally break any of the parts. The caliper posts aren't sealed at all, so if this is a chainstay-mounted break, it's likely that a bunch of grit got in there and is making the post/brake body interface gritty.

This newer generation of brake may also be flange-riveted at the back of the brake body, meaning it's a one-way fit; once disassembled, it will not fit back together properly at all.