Great - details.
Looking at the pics of the PCB the mounting holes are very small (smaller than the 4mm centre hole of a keyswitch), a round M3 standoff is 5mm outside diameter and an M2 is around 4.3 so the only thing going through that hole is a screw. Do any of the screws fit those holes nicely? If you want to use them that would be a good place to start
Also are the numbers after the - the length of the screws?
The other option is to ignore the holes and hold the PCB using the layers. As you're using hotswap you probably want to use a 1.5mm layer for the plate so the switches clip on and don't fall out easily. With 1.5mm for the plate and assuming the PCB is 1.5mm thick a 5mm case layer would go down to level with the bottom of the PCB so if the next layer had a smaller hole so the edges touch all round the PCB it couldn't drop any lower. That layer can be 5mm as well, and if the hotswap sockets don't stick out more than 5mm you just need a bottom layer.
So 5mm holes in the case layers and 4x5mm layers means you can use a standard '20mm M3 round standoff' -
like these which will leave you 1.5mm of exposed screw but if you put that at the bottom it shouldn't be noticeable. Or you could use 2x3mm middle layers below the PCB for a slightly taller and more expensive option with less screw showing. Or if you want it really chunky you could use 2x5mm layers below the PCB and use a 25mm standoff...
M3 is a standard size screw so you should be able to use the screws you have, assuming they are just different lengths.
The only worry is that 1.5mm acrylic plates can be fragile. The PCB will be taking some of the load when you use the pad but I guess you're planning to swap the switches often which might not be ideal.