Standard M6 screw heads would leave little material under the counterbore, so I bought some low-profile screws. I doubt they're as strong as the standard ones, but they'll be fine in this application.
Drilling new mounting holes.
Yeah, it's a 12mm end mill not a proper counterbore. But it's an end mill I've got and not a £20 counterbore I don't.
I'm sure it's leaving the counterbore slightly crowned, but it's good enough.
One hole made and the trial fit looks fine.
There's 1mm between the bottom of the encoder mounting plate and the bottom of the table.
I'll need longer wing bolts for the locks. Or thumb screws? Star bolts? Whatever they've called.
The encoder cover in the worst-case Y position still leaves some clearance for the wheel.
Checking the encoder is parallel to the table.