Even if this happens it won't make any difference to how these instances operate, will it? It'll just reduce traffic to them, right?
It's the same effect as any platform that tries "free speech" invariably becomes a nazi echo chamber, because the only people who WANT to use the less popular system are those that CAN'T or REALLY REALLY REALLY cling to their ideology.
So indeed, most people (normies) will naturally flow towards larger and more mainstream instances. It's already tilting in that direction and actively encouraged in the signup process.
As these instances grow, they will simply have more disagreeable posts (from the perspective of the ideological instances) leading to even more defederation, hence the split will become ever harder over time.