There are several issues that make the lack of Fire-types so much more glaring than any other typing exclusion (tho, I agree, not to unplayable levels, tho DP do have big issues):Things. Stuff.
-Gen 1 kinda gets a pass since GF didn’t fully know what they were doing
-Ghost, Dragon, and Ice have traditionally been rarer types restricted to later-game, while Fire has been a starter type since inception, and even beyond that has been more common than those three.
-The teams for Agatha, Clair, and Glacia still fit much more thematically than Flint’s; Agatha’s Golbat, and to a lesser extent Arbok, fit in nicely with the Ghost-types (plus they’re all Poison-type), and Clair and Glacia still have full-teams of their respective typing (besides, it’s not as if having NFEs alongside their FE stages wasn’t a thing with other Gym Leaders of those Gens). Flint on the other hand (as well as Candice and Volkner) just feels like he got a couple of Fire-types, then slapped on three random Pokémon with Fire coverage and called it a day.