if you use a lave bucket for fuel in a bronze or steam boiler, or the large boiler with an item input hatch, you can't extract the bucket. AE2 storage busses donesnt recognise there being any slots in it, item pipes (either from MI or modern dynamics) cant extract them, hoppers cant
Curiously, Computercraft computers can recognise item hatches as being an inventory (though I havent tested whether they can transfer it to another container because ive forgotten how to do that)

unless im missing something, as best as i can tell there is no way to extract the bucket that doesnt require the player doing it by hand

That is intentional. You are not meant to be able to use lava as a fuel for boilers aside from manually.

this should be stated somewhere in the guidebook then