In a play-through it isn't necessary to worry too much about type coverage, balanced stats, team roles etc. because the games are relatively easy. This can lead to meta-gaming which may be something you want if you are inexperienced or are trying a challenging game variant like wedlocke challenge for example but takes away from role-playing somewhat. I understand your concern however but teaching Noctowl Fly shouldn't be a problem and if it is that's part of the fun.
Noctowl has an attack bst of 50 and a special attack bst of 76 so is clearly better suited to a special set. Given the limited typing granted by it's naturally learnt moveset of only flying, psychic and normal moves it wouldn't be a problem to teach it Fly. In fact, given that the most powerful flying type move Noctowl can naturally learn is Air Slash with a power of 75, Fly is necessarily a drawback to Noctowl's moveset with a power of 90:
- Opt for a physical STAB attack to deal with special tanks
- Dodge attacks in double or triple battles from your team mates
- Allow your opponent to take damage from a status condition or weather effect etc. whilst avoiding taking damage
All this being said you can just catch two Pokemon to be hm slaves and switch around the rest of your team, obviously with six members of your normal team for boss battles be that against rivals, evil teams or gym leaders etc. but it isn't needed at all.