Yes, installing your own cert into Code Integrity is possible (in several ways, actually, but I did it using HtcRoot just as an exercise). The certificates are actually stored in the registry, so any tool that can write to HKLM can add them. I believe that WP7 Root Tools will also let you choose the store for adding a certificate if you "open" the cert from the Root Tools filebrowser.
Although I don't know exactly how HtcFileUtility works, here's the basics. It's a software driver that exposes an interface - probably an IOCTL - which apps can use to perform filesystem operations. Since it runs with TCB permissions (it's probably kernel mode, though I haven't actually checked, but it's definitely in TCB) it can perform any operation that the filesystem supports. Of course, that doesn't mean that it exposes all those operations through the IOCTL... but it exposes enough of them for a pretty solid filebrowser implementation (that's how TouchXplorer and Advanced Explorer worked, although they used an OEM COM DLL that called into the driver rather than doing the IOCTL themselves).
The new version of it has very limited operations permitted; it will only list files in a few folders and so forth. It does still "work" within those limitations - Connection Setup, for example, uses it to check the folder that we use for interop-unlock on HTC - but it isn't useful for a general-purpose browser anymore.
It would be great to even figure out how to roll back the OEM drivers to earlier versions. For example, I've got WP7 Root Tools installed on my HD7, but I don't want to install HTC updates because they'll break my drivers such that if something ever goes wrong I won't be able to re-install Root Tools, or if a new hack is found (or developed; I'm working on some stuff with HtcRoot still) I won't be able to run it on my phone. Being able to use the advantages of the new firmware (Internet Sharing, compass in managed apps, hopefully an end to the damn music player freezing between songs...) while still having hackable OEM drivers would be reallllly nice...
Win8/Windows RT Projects:
List of desktop apps for hacked RT devices
XapHandler, Root Webserver, OEM Marketplace XAPs, Bookmarklets collection (Find On Page), Interop-unlock hacks.