Does getblockcount return the correct block count when running in prune mode? I am currently running a bitcoin node with prune=550. 

The getBlockCount from $ bitcoin-cli getblockcount does not match https://blockexplorer.com/api/status?q=getBlockCount.  As I understand it, the bitcoind is still syncing the node since the bitcoin-cli getblockcount is rising at a steady pace.

Will the getblockcount from a node running with prune=550 eventually match the official getblockcount?
Yes, it will match. getblockcount is the number of blocks that you have already synced to, regardless of pruning.