Baseboard goes over shiplap.

Typical installation is base over shiplap. Like Klem1 said.

But you can also let the shiplap be its own trim to the floor and just run your base to it.

typical base is 1/2"-5/8" thick while typical shiplap is 3/4" thick. Your base would finish nicely I to shiplap. While perhaps the added depth would make the base stick out from adjacent casing. And a tacky back bevel won't do, you probably don't know what a painted end or mitered return are.or how to make them.

what is the scenario? Corner to corner? Section of wall? End wall? Middle of wall? Fireplace wall?