When purchase from Steam, your Steam account will acknowledge the FFXIV in the library and allowing Steam Overlay. You will be provided with FFXIV registration code. You will need to create new Service Account with your SE ID - which will include 30 days game time; You can log in using existing Service Account, but the game time will not be included or added. The FFXIV registration code provided via Steam purchase is theoretically usable by anyone, not necessary be Steam account tied.

It is quite unlikely in near future to have ability to merge different Service Accounts together.