The holes aren't added afterwards: it's a completely separate design of base:
(Yellow with LED, NOS from AliExpress, versus a non-LED yellow from a Zenith keyboard.)
It won't be to prevent switchplate wobble — they're a tight enough fit that even if you break the melted lugs that hold them together, they'll still remain together when pushed back into their slot. The legs of SMK switches aren't wobbly when not sealed, either, but they're far easier to (re)assemble when the legs are effectively glued in. It's got to be something to do with the soldering process. Pin in paste, I know nothing about, but wave soldering has the solder go where there are no solder pads. It's beyond the current limits of my understanding.
There are a few designs of switch with wobbly legs that aren't glued — I guess that the solder puts a stop to that.
Alps LED versions have their own model number range. SKCL for example:
Range A for non-LED (grey is SKCLAQ, yellow is SKCLAR)
Range F for LED (yellow with red LED is SKCLFQ)
Range J for alternate action (grey is SKCLJC)
Range K for double action (SKCLKB)
The part that's confusing me is why SKCC Tall Cream is SKCCAF, and SKCC Green is SKCCBK. I'm wondering if the A range is tall, and B range is short. We have all of two confirmed SKCC model numbers so far, so that's not enough. SKCCAC exists but without a picture.
Cherry also supply factory-fitted LED MX switches, with a different shell (used in Cherry's own keyboards, such as the G80-3700); the difference is chiefly the ledge where the LED sits. When I asked Cherry US, they knew that the factory-fitted LED version was a different shape, but nobody remembers why they did it, and why the normal switch is somehow suitable for everyone else fitting an LED, but not Cherry. It's a mystery!