It strongly shifts the balance in favor of Quantums. Depending on your boff setup, the extra punch of Quantums in something like a torp spread may be more useful no matter the projectile doffs you're using, but it's been a while since I've used torps at all to test ._.
The main issue with transphasics in STFs is that their benefit is shield penetration with the tradeoff of lesser damage. However, a lot of objectives in STFs (Nanite gens/transformers, gates, the cube healers in Cure) have no shields, and the Borg with shields are primarily hull tankers. The transphasic special ability is thus mostly wasted, leading to a much less optimal use of that weapons slot. A photon or quantum (or maybe plasma?) would serve far better in the damaging role.
This is not correct, it depends ont he number of Projectile Doffs you use.
1 Proc from a Blue Doff will allow a photon to contstant cast, the same can not be said for a Quantum, as you would need 2 Doffs to trigger or you still have a 3sec CD on the weapon.
If anything, Photons are actually better than Quantums with the Doffs.