More CA config fixes: sync logic of writing of output collections with old-style

Sync writing of NCB_MuonSegments and EMEO_Muons logic in CA with old-style config (should remove some differences).

Tested locally with MuonConfig and MuonCombinedConfig unit tests, and with q445.

Will not run in production, so will not change outputs.

cc @elmsheus @nstyles