It's a tradeoff, like many in Civ games. Devoting production (or gold) to have a stream of missionaries to re-convert your own settlements means not spending that production (or gold) for overbuilding your Antiquity buildings. Not overbuilding means that your yields will be lacking, making it hard to achieve the Exploration Science legacy path, to have non-city-center districts with amazing yields.I think people underestimate them. You do need to produce or buy a stream of missionaries to keep them converted, but I think it’s arguably worth it, especially as you can get those civics fairly early in the Age.
Yes, you unlock the social policies that provide benefits for your own settlements with your religion early. But it's hard to KEEP your own towns/cities converted. Literally every other player in the homelands is trying to snatch them away.
In my last game, I kept about 3 missionaries sleeping in my cities until the age progress hit 90-95%. I reconverted my cities so they would be following my religion in Modern. I can't tell if that provided any benefit other than aesthetics.