So the Releases file looks correct, it's showing the checksums for both the uncompressed Packages file that's not included, and the Packages.gz. This is consistent with how it's done in the Ubuntu archive, where we also don't ship uncompressed Packages to the mirrors but include them in the Releases. So looks like this is an apt bug only.
The Releases file shows:
MD5Sum: 460177843ff5d2b 3e6 103 restricted/ binary- amd64/Release 1faf4c6e648bef2 bac 1417 restricted/ binary- amd64/Packages. gz 8358681be526e26 ca3 3347 restricted/ binary- amd64/Packages d4202dae7dbaf18 cc2 96 main/binary- i386/Release 3b3f76a2378a450 4aa 20 main/binary- i386/Packages. gz 04e9800998ecf84 27e 0 main/binary- i386/Packages b64d9119c8727cd a8c 97 main/binary- amd64/Release 5a55ae27e814061 e59 9421 main/binary- amd64/Packages. gz 997d475f4dc1a8a d27 29664 main/binary- amd64/Packages
97ecff09a695f1
6541d021d179f7
6f17e84edd2648
b6aa9a96c765bb
4a4dd359870760
d41d8cd98f00b2
846e0e856bcbf9
6ef398509f423f
94df072b9fc141
[etc.]
So the Releases file looks correct, it's showing the checksums for both the uncompressed Packages file that's not included, and the Packages.gz. This is consistent with how it's done in the Ubuntu archive, where we also don't ship uncompressed Packages to the mirrors but include them in the Releases. So looks like this is an apt bug only.