Yes, I have encountered various issues with the various profiles that are available for keyboards with Cherry mx compatible switches, including the cruciform stems on the Topre-switch CM Novatouch.
For example, I have found that some stabilized keys on a WASD keyboard do not bottoming out correctly with thick PBT caps in "Cherry" profile and Cherry profile keys not bottoming out correctly on some rows of a KC60 board. In addition, to avoid bottoming out noise on the Novatouch, I have found that OEM profile works best.
My understanding that the true Cherry profile is found on original Cherry keyboards and keysets made by GMK.
Thus far, I have found various distinct profiles for Cherry mx (or clone) switches:
+ Cherry
+"Cherry-like"
+ "OEM" (Filco, etc. profile)
+ Gateron
+ Leopold
+ SP (DCS, DSA, SA)
These various profiles can cause problems when you are trying to match profiles when using two different sets on the same keyboard. For example, I like to use blank black modifiers and a contrasting color for the alphanumeric keys. Sometimes two sets that are advertised as "Cherry profile" do not match in height when installed on the keyboard. You have to look at both the skirt length and the stem length relative to the skirt length of the cap. If you compare heights with the keycaps on a flat surface, they can appear to be the same height, but if stem lengths are not the same, the caps will sit at different heights when mounted on the keyboard.