Don't "worry", Angel's Petrochem fixes this, and IIRC all the products can be reduced to syngas & produced from syngas. If normal oil ever gets too easy, Angels will literally melt your mind. No flare stacks that's cheating ;-)
More seriously, this is why I enjoy some of the mod packs. The loops in things makes things harder, so now you have to really manage the by-products better. E.g., Bob's has a nasty challenge with sodium hydroxide, a by-product of chlorine production. In the early came, it can stack up, & become a real pain. In the late game, LDS production eats it alive, so much that you actually need to appropriately vent chlorine.
I also appreciate playing Bobs/Angels in a sort of "try to waste/vent as little as possible", which means I need some more complex designs, normally to say "if we have waste by-products, use those, else, generate the product directly".
I wouldn't want it in the base game, though, that's a bit much for new players. But the challenge exists.
There's also a bit of fun w/ sulfur dioxide/sulfur in Bobs. You get both as products, and you need both as inputs, and you have to balance the production. (Or, you can just turn sulfur into sulfur dioxide & vent it, but that's boring.)
The other bottleneck that bites me (and that has bitten me in my current game) is pipe throughput. We're going to have to re-layout some stuff, as we've hit the upper bandwidth of our current pipes, I think. Rocket fuel just eats hydrogen like crazy in ammonia/hydrazine production…