Yeah, bridges across major rivers will be impossible in most cases, but I'm ok with that since they blocked boat travel anyway. And trying to get boats crossing bridges without looking horrible is tricky.
As for religion crossing rivers, the way religions move across regions is actually changing. Cult influence will only be transmitted to neighboring regions within the same province, or along trade routes. No more Maskling cult influence somehow crossing the border despite you being quite hostile to the little jerks.