As in TOH, i guess A3 will include java class files directly inside the mission- or addonfolder (and later inside the pbo) wihout compression.

The problem is that pbos are not compressed by default! That means, a big mod written in java and packed using pbo will have no compression at all, so these files could get really big.

Java's default jar packages are using ZIP to compress java .class files to reduce their size. That saves up to 60% of the filesize. Image you should download a >10MB Mission.pbo...