Ah, another member of the 100x science crew leaving feedback, welcome :)
It's definitely expected that you're going to be creating lots of chemical plants and assemblers to make ore. The trade-off to not having to go find ore patches is the need to build out infrastructure instead.
As far as productivity goes, I had previously had the idea to make mining productivity apply to the "mining replacement" recipes - ore/stone from sediment, calcite/tungsten from lava, etc. I ended up not doing it, partly because it seemed inconsistent when there's no equivalent effect on recipes like molten iron/copper from lava, but I might change my mind do that after all.