While it may have been working from a practical PoV (not certain though,
since some bug would prevent clearing runtime data when writing embedded
Scene collection in current code), this is semantically wrong.
The owner of an embedded ID is a critical piece of information in
Blender data structure and ID management code. Having it written in
.blend files is also a potential good source of data for investigating
issues.
Further more, this handling of `owner` ID data is somewhat generic now
in ID management, so if this data should be considered runtime, then the
change should also be made in NodeTree and Key IDs.
This commit partially reverts 44dd3308a5, in the future I'd like to
be involved in the review of changes affecting ID management.
NOTE: fix for embedded collection runtime data not being cleared on
write will be committed separately.
a1507baead