Compatibility problems with x86 phone?
It's mostly games that might be incompatible with x86.  Typically, apps have no reason to use the NDK unless they has special performance or graphics requirements, and their libraries might only be built for ARM.
I don't believe that apps using root are typically incompatible, it's rooting apps &mdash; since they often rely on platform-specific binaries/exploits.  Root apps are not inherently different in how they are coded than others apart from requesting elevated privileges via su.
Unfortunately I am not familiar with Xposed support for x86, but I believe the answer should be similar to #2.  Xposed mostly functions by injecting itself into Android's platform framework, which is Java rather than native libraries.  I would advise you to be careful with backups and making sure your device is relatively easy to flash if you need to restore everything to stock.