The factory fit clutches attach with machine screws into tapped aluminium plates bonded into the deck. The plates are located in the flat areas where the clutches are, so you can only fit additional clutches if there is spare flat area - for example my 33 has space for 4 clutches either side, and I have 4 fitted on port but only 2 (for the mainsail furling line) on starboard, So I could fit another 2 if needed by drilling and tapping into the plate.
If you do want to fit something off the area where the plates are then as you say, you would expect to need to through bolt which means access to the underside. To do this you can either cut a section out of the liner and turn it into a panel to cover up afterwards, or drill holes for access just where the bolts will be and use some form of plastic plug to cover it.
What Konan is doing is relying on the selftappers and the adhesive properties of the Sika. The load of the traveller adjusting line is relatively low and is in sheer so this works - although I perhaps might have used epoxy in the screw holes as well. Not sure I would use this method for attaching clutches, although there is a method of creating what is effectively a threaded insert in the GRP using epoxy - well described in the West systems book. I added an extra clutch for the main halyard to the mast, rather than have an extra organiser to lead it back to the cockpit, and I drilled and tapped into the aluminium, but it is only full threads deep. As it is a furling sail there is no value in adjusting it while underway, so I made th halyard long enough to go back and added a turning block to the base of the mast so that I can lead it back to the cockpit winch when I install the sail.