Not exactly sure what your comparison is but some thoughts
Once Backup Exec's Agent for Windows is installed inside a VM a modification is made to the pre-freeze and post freeze script files relating to VSS snapshot providers within the OS of the VM.
These script files are used whenever a vSphere Snapshot is requested (or deleted) as a call is made through the VMware tools which calls the scripts - it does not make any diffence if Backup Exec initiates the vSphere snapshot or if another product does it, the change due to the install of the Backup Exec remote agent is still made (and then undone when the vSphere snapshot is removed)
This has been known to cause problems if you mix:
- Backup Exec vSphere Backups
- 3rd Party requested vSphere Snapshot changes
- Traditional agent backups of the same VM using Backup Exec.
the problems might affect CBT (so incremental backups) and / or or cause outright failures - as such some examples
1) if a traditional agent backup of the VM is running, then any call to create or remove a vSphere triggered snapshot at the same time will cause the traditional agent backup to fail.
2) Extended chains of snapshots may cause delays that result in a timeout (irrespective of other load on the server)
3) Incremental backups may run as fulls (or fail depending on settings) if CBT is unexpectedly changed between the full and incremental backups.
You do therefore have to take care with scheduling etc to avoid any conflicts or any breaks in the sequences of incrementals back to the full.
Note: As far as I am aware, VMware don't recommend maintaining long running snapshots due to the potential for adverse effects on performance and suggest these are only used for backout plans for change control practices or similar.