I am not aware regarding crosses being built below ground level, however in Bulgaria all christian churches built/renovated under the Ottoman rule had to follow strict policies:

According to the Ottoman laws and regulations, the church should be very modest without a bell tower or ornaments and not taller than the Islamic buildings in the town or village.

Some Problems of the Religious History of Bulgaria, page 5

Now, in order to adhere to these rules a lot of churches were built with the first floor being below the ground level. I've personally seen such churches in Bulgaria.

For example the church of St. Konstantin and Elena has the first floor below the ground level.