How old is the boat? If new, then it is probably construction residue left behind by the tank manufacturer. If older, then it is probably junk that has settled out of the fuel over time.
Did your last fill-up include the new E10 (ethanol) blend? If so, the ethanol is a solvent and will loosen the varnish that settles out of the fuel onto the internal surfaces of the tank and lines. That could be your problem. If that is the case, be patient and have a lot of in-line fuel/water separator/filter elements until the junk is finally out of the tank.
Megabyte (Kevin) has the new Yami 10 micron filter that was shipped to the dealers/service centers specifically to deal with the ethanol problem.
Your mechanic's desire to remove the anti-siphon valve and install an in-line on/off fuel valve is not off-base. The anti-siphon valves have had a long history of problems and many mechanics simply remove them. Not sure what their legal liability is though when they do that because it is a USCG reg that permanently installed fuel tanks have them.