I am not Marek or a part of Qubes OS core team and I can not talk on their behalf. Just an ordinary forum users like others.
Having said the above, for people who did in-place upgrade of their Whonix 17 to (Trixie based) Whonix 18 and if they want to update their apt files from the old .list format to the new .source format, Whonix project provides a nice repository-dist bash utility which automates this conversion.
In Qubes OS (native) Debian template case, since Debian 12 is still supported, It might be the case that maintaining two versions of the file is harder than just having one and less problematic. But again, this is my personal hypnosis.
Once we don’t need to support Debian 12 anymore, we can migrate to the new format. Old format is fully supported in Debian 13 too, so migrating now is not strictly necessary.