No, not all file versions count against your data limit.
A Baseline file is created. Then when the file is changed, our software calculates a Delta (the part of the file which was changed). The Delta is uploaded to our server and the newer version of the local file is cached. When a new change to the local file is applied, the second Delta is generated and uploaded to the server, and the whole local file is put to cache again.
When doing a recovery from the cloud at this stage, our software retrieves the latest Baseline + the latest Delta from the cloud and merges them.
A file is fully uploaded (new baseline is created) when the new file is more than 50% larger or smaller than the initial baseline or the cache is cleared.
We count Used Space against the data limit as a sum of MAX Baselines only.