Uchiha being composed by multiple internal factions is interesting- given they are prone to strong emotions, it actually make sense.
Then charismatic strong leaders appeared and they did bundle together(though I suspect the presence of the horribly overpowered Hashirama might have been an even bigger motivation)
Also, I wouldn't trust a word said by Tobito. Even if HE thought he was telling the truth, Madara and\or Black Zetsu likely lied a lot to him.
Madara never letting go the Hathred was useful to Tobito's narrative for Sasuke: if he told him Madara and Hashirama actually were mostly on the same wave-length and everything did fall out because of long-lasting grudges, Sasuke could have decided to re-join Naruto as the idea of the mutual village DID work, if far from perfectly- it would become just a matter of "doing things right".
Also, the "official history" seems to suggest the Uchiha were the main force behind the creation of the Village, with the Senju joining them, while from the Hashirama flashback it's the reverse. it might have been to "keep the Uchiha happy" while not giving them any power.
About rallying different clans together:
It's quite likely that the bigger clans had a number of satellite clans, probaly depending on the geographical zone of influence, too.
For example, a Clan A might have a strong presence in Country X. They get defeated by the Uchiha but instead of being annihilated, they accept to become their underling, keeping their position as Country X top dog but sending part of the gains to the Uchiha, as well as assisting the Uchiha clan in various ways.
Smaller clans might be directly absorbed in the Bigger clans, especially if they had good genetics.
I actually suspect the Sarutobi+InoShikaCho Clans is somehow different by being a "true" alliance between three clans under the Sarutobi clan as leader.
A sort of small scale Village: they were independent but coordinated together for maximum efficency.
also, fanfic idea: when Madara tells Hashirama the only ways he'd join in on the Village Idea, a Random Senju kills Tobirama because the Senju are tired of fighting, too, and they all did know Tobirama's "skeptikism" of the Uchiha would become a problem if they were ever to join in a Village