They are very different from my point of view. Maybe that is my bad. Option 1 was 2 separate drives entirely. Oprion 2 was the 2 drives effwctively 1 larger drive with a partition. The aim being 3 fold. Speed, if a drive fails only part of the system is corrupted or lost, 3 ease of repair or reinstallation.
Speed is not an issue with either configuration.
"Ease of repair or reinstallation" is handled by a comprehensive backup routine.
Full drive(s), automated, Images saved to some other location(s).
Automated and tested.
Right now, if any of the 6 physical drives in my system were to die, all I'd need to is slot in a new drive, and recover from last nights backup.
Poof, contents restored exactly as it was sometime between midnight and 5AM (2 hours ago)
With the OS on one drive and applications on another, or all on the same drive...it makes no difference.
In the event of an OS install, you'd need to reinstall the applications anyway.
Your data, OTOH, can easily live on other drives.