Time Machine?

Greetings - I've not used Time Machine for my professional work ever and only used it for personal items many years ago with a Time Capsule . . . that seemed to have more issues than not.

At this point I recently had to replace my 960GB PCi-E hard drive . I have a 1TB spinning disk drive in the second optical bay that I've used in the past with Chronosync to make and maintain a cloned bootable back up of my PCi-E hard drive.

I looked at Time Machine again as that was what the Apple Certified Service Center was using and just did a full backup with it to the spinning disk.

Running all this on a 2012 era MacPro with latest version of Sierra, six dual core processors and 64GB of RAM.

Are there any issues that anyone is aware of with using Time Machine for the primary OS drive?

I still use Chronosync to mirror my two RAID setups for project content, FCPX libraries and what not.

I can't speak specific to the Sierra OS as we are still on El Capitan. But I do use time machine to backup our OS which is also a 960GB SSD on a PCI-e card and it seems to work very well. I also clone the SSD with CCC to another external drive. Over the past two years I have had to restore the OS twice and did so from a time machine backup which worked very well. The only issue I found was the need to then reimport the mail folders, and while all the email data was intact, the individual folders were no longer sorted alphabetically and required a bit of rearranging. Other than that, just a few simple reinstalls of some minor apps and plugins were necessary. It seems to be a pretty painless way to reinstall the OS to a new drive. (at least under El Capitan and previous OS's). We run Time Machine manually once a day, but otherwise it is turned off and the Time Machine drive is a 2TB drive in the SATA bay of the Mac Pro.

If you use TimeMachinem, I'd recommend leaving it off while you're working with FCPX or other process intense apps, burn i back on when you're done. We use Carbon Copy Cloner. 3x restored from backup drives to OS drives with no issues at all. It does incremental backups nicely, too, since it recognizes OS X "package" content (such as an FCPX Library).

Ben added

If you use TimeMachinem, I'd recommend leaving it off while you're working with FCPX or other process intense apps

and more...

We use this little software to control the Time Machine activity.
tclementdev.com/timemachineeditor/

As I read the question, the OP is asking about using a Time Machine formatted drive as a Boot Drive. That is a no-no. It is really designed as a back-up drive, not to be a boot drive.
Go grab a new drive, ssd preferred, or hdd, stick in a sled and slide into a SATA slot and format as macOS journaled, and then either use TM to restore data or go clean install, OS, apps, plug-ins, and then drag files as you need them.
Personally I do the later.

Hope this helps, Greg