The rest of your post I agree with (and yes, rectifier/filter supplies can have very low PF, though a 3D printer won't have such an old-school design), but I don't think so about watts and run-time estimates. The UPS has to generate apparent power, and the imaginary power component is still lost as heat (within the UPS). Sure, at the battery side of the bus the draw is in watts (it's DC), but the UPS conversion efficiency will vary with the PF, so I'd guess that the battery real power draw more closely matches the UPS apparent power output (AC VA) than the UPS real power output (AC watts).
Yes, most electronics these days have power factor correction and a good PF, probably 0.9 or better. So the whole discussion of VA or watts, in most applications, doesn't really give much different results.
But technically UPS run time would be most accurately based on watts. Here's a ups manufacturer run time chart.
https://www.cyberpowersystems.com/tools/runtimes/
Nowhere is VA found. The imaginary power isn't all lost to heat - it goes back and forth between the load and battery/bus caps. The ups will have more losses with a poor pf load for the same watts. But those additional losses are going to be small compared to the load wattage. Consider a power factor of 0.8 with a load of 1000W. VA would be 1000/.8 = 1250W. The load current on the output will be 25% higher than for a PF of 1.
PF of 1 line current for 120V power is 1000/120 = 8.33A RMS
PF of 0.8 line current is 1250/120 = 10.4A RMS
If we estimate the losses in the inverter to be 10% (which is likely more than it is - I design small inverters this size for mass market, cost sensitive applications and they are typically 95 - 98% efficient). Thus the losses for 1000W would be about 100W (worst case and likely much less). If this loss goes up proportional to the current (a reasonable approximation) this would be an extra 25W loss (125W total loss).
Total of inverter and load power (loss) for PF=1 is 1100 W.
Total of inverter and load power (loss) for PF=0.8 is 1125W.
The change is 1125/1100 = 1.023 or a 2.3% increases in losses.
This is probably within the accuracy of the run time estimate and nowhere near the 25% increase that just using VA would give.
Note that there other losses in the UPS front end and battery but those will be affected by PF even less if at all.