As IHO said, electrical and structural need to be upgraded with builder because you can't really do it after COE.
For my wife, kitchen is the most important feature in the home, so waterfall island, kitchen countertops, stacked cabinets and cabinet doors/handles, are a must with the builder.
Flooring is also a must, but that depends on the pricing the builder offers. We would prefer to do it with the builder because no matter how good the contractors are, doing flooring, especially tiles, after COE could cause problems, like damage to the walls. In fact, if you have a stand alone tub in the master bath, contractors wouldn't want to move it. So in our current home, we decided to do tiles (24" x 48") in all baths upstairs and laundry room with the builder. We use the same tiles (polished porcelain), but 48" x 48", downstairs, after COE, since Shea charged a lot more for flooring than 3rd party.
We also upgraded all the shower/bath walls to 24" x 48" polished porcelain tiles, same as flooring, to the ceiling, with the builder.
For us, if the price difference isn't too much between builder and 3rd party, we would prefer to do it with the builder for convenience. It really doesn't make sense for builder to charge more than 3rd party because they save on the standard materials if you upgraded and they probably have some kind of deal with the vendors on the upgraded materials. The other thing is that they have to put in the labor regardless if you upgraded or not. 3rd party would actually put in more labor because they need to rip out the old flooring. And yet, Shea quoted almost twice as much as 3rd party on the flooring, so we had to go with 3rd party for flooring.
TLDR: We desire full upgrades
and would prefer to go with builder if the pricing is reasonable. Actually, when we bought the first home in Irvine, we went with full upgrades with Irvine Pacific (they were more reasonable with pricing) because we were moving from Eastvale and wouldn't have time to deal with after COE upgrades.