I live in San Antonio Tx. My service weather head is below the roof line. The electrcian says he must drill
Through the roof and extend the conduit 3' above the roof, must he make this hole according to nec. Or san antonio specs. It's a 200 amp

Down here, it used to be 3 feet, it is now 4' through the roof.
Make sure they slide the boot over before the weatherhead and wiring is connected.

But I was told if the weather head is 12' it doesn't need to go through the roof

I would Ask a Local Electrician or look around your area to see what method is used.
A Lot of People will "tell" you things, doesn't mean they are correct, were they a Licensed Electrical Contractor, or did they work at a store?

Also, down here, If the total length was 12 feet, then the 10' length needs to be at the top, then you need a 2 foot length and have it threaded.

but i was told if the weather head is 12' it does'nt need to go through the roofIt's not the weatherhead that matters, it's the point of attachment of the service drop and the subsequent clearance under the drop.

So how high is it now? And what does the drop pass over?