In order for Backup to store application DEBs in backup files, those DEBs would have to be cached on your device at all times, ready and waiting for when you run a backup. So, that's precious space lost there, plus more space lost when the DEBs are copied into the backup file.

Then, when you restored a backup containing application DEBs, the system would need to recalculate all dependencies in case you had done something like backing up on PR1.2 and restoring on PR1.3. And if you had, underlying system packages would have changed, so you'd wind up having to download updated applications from the PR1.3 repo to meet dependencies anyway.

Take, for example, Tweak Flash Version. There's a PR1.2 version, and there is soon to be a PR1.3 version. Using the wrong version on a given firmware revision level can lead to a broken Flash plug-in, so the Tweak Flash Version DEBs explicitly specify a given PR version in their dependencies. So, if Backup saved DEBs, when it came to restoring Tweak Flash Version, Backup would have to refuse to restore the PR1.2 version and force you to download the updated version for PR1.3.