Sealing the box into the fender is a non issue. You will not find any water/moisture blowing into the trunk from underneathe through any of the 4 sides assuming the box is a good fit, as yours is Saiid(along with every other pic posted of folks who have done this). The roost from the rear tire sprays up in the center, and any water contacting any of the four sides of the box would have to have pressure washer force to get water up over the top of the box and thus running down into it. The problem is as always, the rear seat/hump. Water will blow into the stock or modded trunk from above when riding in the rain(between the tail plastic and bottom of the rear seat or hump. There are several ways to prevent this(spray foam, weatherstripping, ect.), but no quick and easy way. A drain hole in the stock or modded trunk is also just a way for water to enter from below from tire roost.
There is also not a quick and easy way to remove the stock undertail(even though it doesn't have to be removed to do the trunk mod). The easy way is to cut a groove in the undertail to allow the rear master cylinder hose to pass through it so the undertail can be removed. Otherwise you are disconnecting the hose and bleeding the rear brake.
I have also made and sent 2 free trunk boxes to two memebers a year or more ago, both were 4.5" deep. One member had no issues, the other's rubbed. I have posted before that it's not only rider weight, or rider and passenger weight, but how you have the rear suspension set up. Too soft and you'll have issues, and of course if the bike is lowered.
I'm 195lbs in leathers and have set the sag, and even with my wife on the back my 4.5" deep box does not rub.
As posted before, if the box is too deep, remove it and trim a half inch, an inch, whatever evenly across the top and reinstall it. Black plastic license plate bolts also work well to hold the trunk in.
I have been dwelling on this idea for years(even before putting the first one in a gen2), and I have yet to determine how to make this a generic part without rubbing issues...without the box being more than an inch or two deep.
It is as you see much more than the average rider wants to do to their bike, regardless how easy it really is.
The cost of a patented version in different depths, be it trunk only or complete undertail far exceeds the cost of a trashcan and an hour of your time. I looked into that too.
The Tiger Racing undertail was built off of the trunk mod idea, but I respectfully say was disapointing to many as it is basically a race only or fair weather application. As it is not sealed from underneathe at all.
I said originally that I like the fact that ideas are built upon, and I'm very happy with all the positive feedback and individual variations seen so far. However we are still at square one for a cheap generic version. I won't be the guy to say it can't be done, but for a $7 trashcan and a little time I don't think there is a market for something that would have a high pricetag; especially with overhead and shipping costs of a full undertail added also.
The challenge remains.....................