I use the very fine glass-head pins also, as when you stick the pin into the fabrics it disturb the seating of the two pieces of fabric less, in my opinion. But I insert them back from the path of the foot whenever possible, and depending on what I am holding together, I pull them out and adjust the fabric well in advance of reaching the foot because pulling a pin out on the last second can cause the top layer to pull back a smidge.
Sewing over them? Not any more!
