This falls in line with the OS Optimization Tool, which can also break things in certain circumstances. Just like OSOT, CIS needs to be implemented in a way that is catering to VDI. I haven't ever done it personally, but I wouldn't be surprised if some of their benchmarks lock down things in a manner that is incompatible with VDI. Also just like the OSOT, you'll likely have to carefully test and retest these settings.. You can make your own templates in OSOT which may be a good starting point for this process.