Here is a quick update. I ordered several rubber sheets with varying thicknesses and materials. After testing the materials, I decided to go with a 1/16" thick Neoprene sheet. I then used a MX switch plate I had laying around with matching spacing on most rows to mark the cut-outs for the Topre switch housings. I had to move the plate around to get the 4th row and some of the bottom row keys, but it mostly worked out without needing to take measurements. I then used an X-acto knife with a flat blade to make the cut-outs. It took me most of a Saturday afternoon and I went through about 8 blades, since they do tend to get dull and lose corners throughout the process YMMV. I used a piece of plywood as the cutting surface, so something softer may make your blades last longer.

I am pretty happy with the result so far. The travel reduction is about 2mm. The tactile sensation of the dome is still very much there: only the dead travel from the bump to the bottom is gone. The landing on the mat isn't too hard either: just a bit more rigid than the stock bottom-out feel of the silent type switches. For me, it is pretty much impossible to not bottom out these switches stock when typing, so the reduced travel definitely removes a lot of finger fatigue, and I can endure longer typing sessions with the board now.

There are a couple of things to be aware of with this approach. The first is that you do have to void the warranty and open up the board to install the mat. Once the rubber mat is installed, there is no way to seat the keys properly without pushing from the other side of the sliders as you press the key caps in. This, of course, means that you have to open up the board every time you want to remove and re-install key caps. It's a bit of an inconvenience, but I don't envision doing this very often. If you are unfamiliar with taking apart Topre boards, I recommend looking up a video of how to open up a HHKB properly before doing this, as you may end up with domes and springs scattered all over your floor otherwise. If you plan to lube your slider housings, it is probably a good idea to do these things together.

The second important point is that the mat must be as flat as possible. I recommend checking it several times for flatness before re-installing the keys. Take the time to cut out any parts that interfere with the housings and cause small humps to form, as the these will prevent the entire bottom surface of the key caps from contacting the mat at the same time, leading to uneven bottom-out characteristics and mushiness. It's better to make the cut-outs too big than too small initially. All that really matters is that they must be smaller than the footprint of the key caps they will be contacting.

In the future, I think much work can be avoided by casting the mat in place using some type of soft resin that can be poured and cured but does not bind to the plastic in a destructive way and can be easily removed if need be. I am not aware of such a material at the moment, but this would definitely speed up the process.