I am starting a new game for morrowind and want to have an immersive playthrough as an Argonian warrior type character, I am unsure if I should use the alternate start mod or do the main quest, To me it just doesn't make sense that the nerevarine would be an argonian.

Well that is purely up to you. You can skip the main quest and do side and faction quests instead. You can also give a try to some of the quest mods out there.

You're asking, but I feel like you already decided. I personally see no reason why he couldn't be an Argonian, but if it would bother me, and if original chargen and quest being available would itch me too much, I'd definitely go for Alternative Start. You can just toss the instruction papers into a corpse and let it all go poof, Morrowind's main quest isn't particularly intrusive in my opinion. Skyrim's mainquest feels like someone is shoving a rock in my ass, so I use an alternative start mod there.