For the random doodads and visual flavor, for example randomly spawning flowers on grass tiles, the visual aesthetics often needs to be hand-tuned. Is there any way to influence the rule application seed?

Maybe a flower spawns here, but I'd rather it be over there -- do you have any recommendations on small tweaks like these?

Yes it can!

Click the "..." on the Rules window to adjust the seed. This is probably good enough for my purposes, at least for now :)