For purposes of SYSTM workouts, I would use the trainer’s power numbers. Don’t worry whether they are the same as your separate meter (I’m assuming your trainer works and power tracks your external meter, even if it differs). Remember: SYSTM will tell the trainer what resistance to apply for every workout. That means it needs to base everything off the trainer’s power measurement. I’d suggest turning off your separate power meter and using the trainer’s for everything. Then do Half Monty again (erg mode for stair steps, level mode after)or Full Frontal. [Some trainers require a spin down process to calibrate the power meter. If yours does, do that first. Mine doesn’t, so I can’t provide much additional info.]
If it helps, think of the numbers as “trainer points” that SYSTM uses to plan workouts customized to your abilities. If happens that trainer points are related to watts, but don’t worry about that. It’s like different currencies. Prices in dollars are different from prices in euros. If you’re paying in dollars, you have to use the dollar price. Roughly following the analogy, SYSTM sends the trainer instructions in dollars when you’re doing a workout, so you have to do the fitness tests in dollars too.
Note that Indoor/trainer and outdoor power are different for most people for multiple reasons: location of power measurement device, calibration or zero-point differences, different body mechanics on a bike attached to a trainer versus rolling down a road, psychological differences, etc.