2004 3.4L GM Deck Height

I think I may have a problem. Head gasket blew. When taking off the heads a noticed severe (deep) machining marks on the decks (probably there since engine was built) and some corrosion around a water passage. Took the engine to a local engine shop. He said he could take some off the top. I said ok. Now during reassembly the pistons stick out above the deck at TDC. is some protrusion as designed? Piston travels .025" above deck now.

How much did he take off the deck, what is the stock deck height, machinist should have this info and acted accordingly!

He said just .006" was removed, and it is normal for the pistons on this engine to protrude from the top of the deck. True??

Don't have the blue print specs, but .006 shouldn't be an issue.