When running bitcoin-qt for the first time, the intro window is shown where the user is prompted for where they want to store the datadir, the default is ~/.bitcoin.
If there's not a lot of space in ~/.bitcoin, the prune option is enabled by default. However, a common use case is to point -blocksdir to a larger partition/drive.
The current behavior as of Bitcoin Core v31.1 only checks for the available space of the datadir which results in prune getting enabled by default even when -blocksdir points to a larger drive.
It would be nice to have bitcoin-qt check whether blocksdir is on a separate path/partition/drive before enabling the prune option. Additionally, this sounds similar to #709 although I'm not entirely sure it's the same issue.