The relationship between the mod scene and scooterist/scooterboy scene has always been a difficult one - fashion and music prerefences being miles apart.
Apart from that the mod scene itself has many of its own sub-cultures from the 79 revivalists to the 60s purists, from ska to jazz, R&B to northern etc etc.
As you are probably aware, the scooter scene is based (obviously) around the scooter, not the music, from cut downs to lights and mirrors to original standard restorations to fancy paintwork with chrome etc engraved plating...it therefore attracts many different age groups with a wide variety of preferences.....throw the mod scene and indeed the skinhead scene into that and you are always gonna get huge differences of opinion, wether based on scooters, owners, fashion or music.
The mod scene moved away from the scooterist scene in the early 80s because of such problems, set up their own rallies and events and even ran 'No jeans, no greens' door policies to prevent scooterists attending....it's been that way for many years, though seems to have settled down over the last few years (whether maturity has had an impact on that is debatable), but many scooterists also moved away from army geens and mohican hair cuts and adopted a more mod look, more also started restoring scooters more to authentic 60s standards and obviously caught onto the wave of 60s R&B that has become more acceptable on the Northern scene in the last 5 years or so.
I suppose dwindling numbers on both scenes, combined with the above facts, have seen more scooterists attending mod dos (and probably vice versa) in the last few years, and bridging the gap so to speak, but these debates and divisions will always arise due to the diversity of the scenes involved.