How do you handle multi-voltage domain crossings during STA signoff?

Treat each voltage domain as its own timing world. Wherever a signal crosses from one domain to another, you put a level shifter, and you check the timing on each side using the voltage corner for that side. In your STA setup, give each domain its own constraints and corners so the tool does not mix them up. The simple rule is to never let one domain voltage assumption leak into another.