It's really a horserace that depends on the application. IRIS tends to favor higher clock speeds, which implies that Intel higher clock speed chips are better. However, Intel makes a LOT of lower speed chips, so buyer beware. AMD does a better job at hyperthreading, and the increased core count can really offset the somewhat lower clock speeds. In an application like TrakCare, where there are many users, this is advantageous. In Health Connect, the higher clock speeds may have an advantage. As always, this is implementation dependent. If in the cloud, you can test both with your application to determine which fits your needs the best. AMD tends to have a slight price/performance advantage.
XFS is the recommended filesystem to use for most cases. It supports larger files, where ext4 has a 16 TB limit. Its journaling is faster. It's optimized for parallel I/O. It's more resilient. Both XFS and ext4 are rock solid.
There are certain use cases where ext4 may be slightly better. The journal file is an example of this. It also is a bit more flexible in certain areas.
We have not been impressed with OpenZFS performance in IRIS, and don't recommend that path.
LVM technology works great, either with XFS or ext4. A large number of our customers use this approach. It multiplies IOPS and bandwidth linearly. You do have to use LVM backup on those volumes.
RHEL tends to be more security focused than Ubuntu, as in SELinux now being standard. As such, their security patches are more frequent, and it's your company's choice as to how often and when to apply these. They are both solid OS's.
As far as VM's go, there is a necessary level of experiience required if using VMware. It's easy to over subscribe and you never want to allow this to happen. There are customers that use one VM per physical machine to avoid conflict. It's all about your production needs.