In FFXIV, anything with an effect over time happens on the server's 'tick.' This 'tick' occurs once every 3 seconds, so every 3 seconds is when you'll see your natural HP and MP regen, DOTs, HOTs...etc.

BLM doesn't have natural MP regen in Astral Fire, so it's hard to gauge exactly when you'll get mana back after Transposing. If you use Transpose right before the tick, consider yourself lucky because you won't be waiting very long for the regen to hit. If you use Transpose right after the tick, you're going to have to wait the full 3 seconds to get mana back.