2 Encoders per axis ?

Short answer:
Yes, you can use encoders, even 2 encoders per axis/joint, or an encoder and a glass scale, both wired to Mesa/LinuxCNC,
and
Yes, you can have one encoder (usually the one on the motor shaft) wired to drive and a glass scale wired to Mesa/LinuxCNC
and
Yes, you can have new drives that take step/dir pulses and have their own encoder and add glass scales wired back to Mesa/LinuxCNC
and
Within reason, pretty much however you like/need.
As for backlash, the best and easiest way is the last version from above.