Basically backup and syncing are different things.
Things like contacts, calenders, and reminders are not backed up because they sync between devices. There is still a copy of your contacts in the cloud but as a synced file not as a backup.
Things like Activity data, Strava data, game data etc is backed up because it is specific data to that device.
Photos are kind of a special case because if you use iCloud photo library then the photos in the cloud are synced (i.e. they are there to sync to other devices) but if you don't use iCloud photos and your photos are not synced to other devices they are then backed up to iCloud.
Synced files in the cloud will change as you change them on your device (i.e. the changes you make will be synced to the cloud), but if you make changes to a file on your device that is backed up, the backup will not change (until you make another one)
However, none of this is really relevant to your situation, Your phone is telling you you have almost 5GB of space left in the cloud (5GB - 39KB) it's telling you your next backup size is 43 MB, but it's also telling you there isn't enough room in iCloud for your backup, which if the numbers are correct, clearly can't be the case.