Do drop them as many parts you want to freshen up. But likely they will just add it all to the bill.
Dipping is especially effective in getting rust out of surfaces and ready for filler/paint. The heater motor cover on the engine side is an ideal candidate, as are the two headlight inspection plates.
Seams are notoriously difficult, capilar action draws only get a small amount of acid, which is often not enough to eat the rust, but it is enough weep the acid later on giving you back what you wanted to get rid off. Good shops flush (high pressure) well enough to prevent that from happening.
Did you remove all of the slip-on type on sheet nuts? Fuel door? Rubber floor plugs (8 of them I think) the white plastic plugs covering the wax injection holes (2 in each rear wheel arch, 3 or so on the inside of each rocker and 1 on each corner of the rocker, under the car near the subframe mount?
Secondly, it helps to think about how the car will be dipped and where air pockets may occur. Some times a well placed small drilled hole will ensure clean surfaces all around.
It applies to e-coat (zinc) layers even more so.