Cherry's own G84 series has Cherry ML switches and smaller keycaps than regular keycaps. Those are still made.
Cherry ML is not compatible with Cherry MX in any way. There are other key switches that can take keycaps for Cherry MX but those switches are not pin-compatible with Cherry MX. ... And they are more difficult to get hold of and most of them have been discontinued for many years, found only in obscure vintage keyboards.
Kailh has a contemporary variant in its catalog but I don't know if it is used in any production keyboard and I have never seen them for sale.
The keyboards with Cherry MX switches that has the lowest-profile keys these days are
MX-Board 2.0 and
MX-Board 3.0 (the latter being easier to get hold of) but that is because the keycaps are flat.
The home row of keycaps in Cherry profile are the same height though. You can't get any lower on Cherry MX.
Signature Plastics' well-known "DSA" keys are higher.
