Reliable sync is only possible when you use a server as the so called "source of truth". And servers always cost money. One option would be to run a server myself but then I would need to charge a subscription fee for that and it would most likely be more expensive than what Apple can offer on a big scale. This is the approach of Bandhelper for example.
The advantage of iCloud is that most users of ST3 will be fine with the free iCloud offer. Only users with very large libraries will have to get the iCloud subscription and even then the price for 50GB is just 1 Euro here in Europe and this is a size that should fit for most.
What I can investigate into is if it is possible to exclude ST3 files that have been uploaded to the cloud from backups. I don't see a need to include them in the iOS backups and that would free up lots of space for you.