I like the "concept" of the Speed Overrides functionality. However, if you are using supports this feature does not really work. If majority of the layer is support material it may take a long time to build and not trigger the speed reduction. However, if the model material being built on that layer is really small, you would want things to slow down. So SD3 should delineate between the model build time, and the support build time per layer to properly apply this functionality. It would be a great fix.
This is an interesting topic, my understanding of the speed overrides, would be that they would slow down your print so your part has enough time to solidify before the next layer is applied on-top of it. Therefore, if it prints the supports after your part, that's only increasing the amount of time your previous layer had to solidify, and therefore calculating the supports with the layer would be working as it's supposed to.
You're saying that speed overrides are more important for the parts finish, that for small layers you want the printer to move slower. I like the way the system it is right now, I think that keeping speed overrides setup for cooling times is a great system and it's provided me with great prints. My recommendation would be to print at a slower speed in general, this is under the Other tab of the Process settings and see how that works for you.
If you start with a part that has a small footprint that is formed on the first layer but a large overall footprint, one that requires a large support structure to be laid down first, this will not work. If I slow down the whole print, the part will take forever to print. Even going into the manual override and speeding it back up. So the first layer of the model will start to curl up around the edges. Then all the subsequent layers will curl as well. This happens even if I make the gap between the support and model 0 (which sucks to remove supports from). This happens because the small portion of the model layer is being laid down as fast as the rest of the layer but not as part of the layer. That is to say, the "model" portion of the layer is built then the support structures, both independently of each other. If the software slowed down the print of the "model" layer it would help.