I finished my RV14 using that method. It really is not difficult at all and using flox will greatly reduce and cracking issues. My Rocket was done that way 14 years ago and there is no cracking in the build up around the intersection faring.
This is not just a cosmetic thing. We know that these planes gain 10 to 15 knots with all gear farings installed. This demonstrates that it is worth spending time on this critical area of drag. I also fare the upper farings into both the cowling and fuselage, using a flox mixture. A tight fit around the wheel opening is also important. Too tight and it will on a hard landing. Too loose and you lose some speed. A finger width seems to be a good compromise.
Another area to consider is at the top of the gear faring. If your model has the gear legs extending through the aft edge of cowling there is an opportunity to increase speed and also to help with engine cooling.
That opening in the cowling where the gear legs exit the cowling, dumps a lot of air down the gear faring. It squirts out around the upper and lower gear faring and wheel pants. This is not a good thing.
When you have that oblong cut in the cowling for the gear legs, fashion a piece of baffle seal to cover the opening around the gear legs and glue it in place. It will rest nicely on the cowl gear leg openings and remain with the plane when the cowling is taken off.
These items were proven to work when I was racing in the Sport Aircraft Racing League a few years ago.