NP is an implant layer, that is implanted into active silicon, also known as OD (OD, moat, active, diffusion - are all different names for the same thing).
OD is not blocking a connection to M1, it facilitates, enables electrical connectivity from the FEOL to the BEOL.
Connection between OD and M1 is done by contacts (CONT), it's a special name for via, that goes down to diffusion or to poly layer from the lowest metal layer (M1 in this case).
To connect to well, you connect to OD (using CONT) first, then connect OD with well / substrate using well tap (a kind of a via, in silicon, from OD down to the well).