I have, every once in a while, started my autos in small peat pots and then just planted the entire thing in my larger pot - works a treat. If the roots grow through the pot, you'll have NO trouble putting them in their forever home. In order to make SURE you won't have problems with coir pots, water them from the bottom - put your small pots on a tray or saucer and pour the water into this allowing the pots to soak up the water from below... this should help break down the coir.
This isn't really considered transplanting... that would be if you were removing them from their first pot and putting them in another one... so you'll have no worries. And it won't matter WHEN you do it... you could do it now or you could wait until you start to see a hint the roots are coming through the coir pot... but when you DO see the roots start to come through, get them in the larger pot asap.
Good luck!