I don't have a Helix but I wondered previously if this would work:
Physically connect upright bass to Input L, and bass guitar to Input R
Upright preset has a 'Split > Y' block with BalanceA panned to L100, followed by a mixer block with B Level set to zero (followed by my upright effects).
Bass guitar preset: same, except BalanceA panned to R100 (followed by my bass guitar effects).
Then the tuner should be available for both?
I'm chronically umming & erring about getting a HX Stomp. Doubling is my scenario as well, so it's good to hear it's working for you.