I don't think there is a carved in stone right or wrong approach, depending on your specific setup, one might work better than the other but neither is wrong.
For me personally, I try to go the route of installing the mounts to the motor first just for ease of assembly on the engine hoist versus in the engine bay.
With that being said, just a couple months ago when putting mine back together (351W platform), it wanted to be a bitch and not cooperate with the mounts on the motor. When trying to position the motor to engage with the bellhousing dowels, the threaded studs on the motor mounts kept catching on the edge of the tower slots and I was also up against the firewall on the driver side cylinder head so something had to give... ended up taking the motor mounts off, dowel pins engaged, started a couple bolts finger tight, plenty of room on the firewall.
The only slight issue I had was getting the driver side mount back in between the tower and the block because I was hitting the firewall again... end up "rolling" the motor over a little versus lifting it straight up with the hoist to get it back in.
If you have a floor jack or transmission jack, you can manipulate the transmission up / down while working the engine with the hoist to achieve the best alignment.
DJs74