Grand Marlin there are many types of flow coat and how they are manafactured varies greatly, most people have no idea what they are using. Most companies will not even go into detail as to what constitutes up to 15% of the flow coat as they will tell you its proprierty information. Most flow coats are based on a polyester base resin and have high levels of filler, styrene and solvent. It is possible to get flow coat that is based on Isothalic polyester resin, vinyalester resin even epoxy but these are very hard to find in Australia. I have just gone through the exercise of sourcing fire retardent flow coat for our fuel tanks. Most gel coats used by boat builders today are based on CCP or NPG technology, are Vinyalester based, have very low levels of styrene, very low levels of filler, no wax and low if any solvent and as such are far more expensive. Go to FGI and price a kilo of white flow coat and a kilo of Ulratec 1000 gelcoat and see the difference. Old technology gelcoats that where poyester based are like you said not waterproof, neither for that matter is the ployester resin used to build the boat, however most manafacturers of newer boats have been using VE based gel coats for quiet a number of years.
Even a VE based Flow coat with its increased levels of styrene, fillers, wax and solvent will not adhere to a substrate as well as a VE based gel coat and if your using a plain Jane polyester flow coat you will not even be in the ball park, VE being based on a cured epoxy molecule has far better mechanical adhesive qualities (up to 30% better) than anythying built on a poyester molecule.
If flow coat was so good we would use it to coat the boats in the mould instead of gel coat as its cheaper and easy to spray and does not tripe as easy but the high wax content would prevent bonding to the laminate thats why when you use a waxed polyster resin you have to grind the surface before laminating over to ensure you get a mechanical bond.
You may be getting acceptable results doing the repairs the way you are but it still is not best practice.
Prove me wrong based on the chemistry of the materials and real world testing results and I will eat my words, I have access to a lab at work and if you like I will do an excellerated ageing test on a poylester test panel gel coated white with CCP gel coat. Test panel one will have a poylester based flow coat repair, test panel two a vinylester flow coat repair and panel three will have a CCP gel coat repair and you can see the difference yourself if you like, we have the ability to age a laminate approximatly 8 -10 years in about 5 days. I have done this test before for our detailing department down on the water and there is even a difference in the gel coat repair where patch aid is used and as for the flow coated repair there is up to 6 shades of difference between the flow coat and gel coat areas. If you want to test your own methods I am more than happy to test a panel which you have repaired to see the difference.
I also have the facility to test for sheer, flexual and compresive strengths, viscosity, burn test for resin to glass ratio, we have to do all our own independant tests for new materials, new laminate schedules etc and we test and record all through hull cutouts to ensure we meet quality standards for resin to glass ratio and laminates are barcol tested out of the mould, at 7 and 21 days to ensure correct post curing. Barcol a flow coat repair and gel coat repair 10 days after the job is done the float coat will barcole low 20's and the CCP gel coat in the the high 30 to low 40"s (barcol is a measure of hardness) When we have to do a major repair we test the repair laminate in the lab before moving to the job.
Hey I may be wrong but you are going to have to prove it.