i too was concerned about the same situation and i guess there might be a possibility it can affect some setups differently. however, it seems to me after 4 updates (i think) they have worked out a lot of bugs. keep in mind it is still in beta too
i did run into one little issue last night but i am not too sure if it was semi-tethered related, MS or Core Utilities related. right after i installed the semi-tethered i installed Autocorrection Bar. tried it out and decided it was not a necessity, so i removed it. well it did not go completely away. the package was removed from Cydia but it remained anywhere that required the keyboard being used. i have my settings configured as Developer so i can see all packages being downloaded, and take screen shots, in anticipation of issues just like this. unfortunately there was only one package and it was called Autocorrection Bar. needless to say my OCD would not allow this so i restored as new and re-setup everything, including the semi-tethered
so with my current setup it does not appear there are any conflicts with the newer Mobile Substrate or Core Utilities but there's no guarantee that it would be the same with another jailbreak setup. although, it seems they have worked out a lot of bugs since the initial release