To add some bits to this thread, from personal experience...
IF your leaks are due to flexing, it will be difficult to get *any* lens or frame to seal for very long. Flexing is rather common to some cheaply-engineered / -constructed boats, which is why they cost a lot less in the first place. But you knew that, right?
External lens caution: be sure that the material has the strength for the width/length on your particular boat. Note that you trade off strength between acrylic (less bend, more chance of a crack or break) and polycarbonate (more bend, little chance of a break). Also, without expensive surface coatings, the stronger polycarb. will degrade a lot quicker in the sun light.
Gasket material: the author is happy with rubber. I would advise using sealant.
The part of the narrative about "floating" the new lens on the outside surface is VERY important. I would go for at least an eigth of an inch of black sealant. Use a special commercial goop or get some Boatlife "LifeSeal" from your chandlery. This is just about the only commonly-available sealant/adhesive for this application.
Dealing with the mess... leave the protective paper on the new lens, both sides, except where the inside mates to the cabin side. Next, sand the surface of the plastic lens where the sealant must adhere, about a half inch around the inside surface.
After you dry fit, tape off the outside of the boat around the lens edge with 3M FineLine or Blue -- same for the inside of the cabinside edge. Run some wider paper masking at least 4 inches beyond the tape...
In order to get the lens to float at the right heigth and not squeeze out the sealant layer, put small O-rings around each screw hole. Once you have the screws in, do Not overtighten them -- if you are indenting the lens around the screw, back off.
Note that the author told you to over-drill each hole. This is because of the expansion coeficient of the lens in heat and cold.
We did this work 12 years ago, using Lexan polycarb. and it is still leak free - although we do now have to polish out the surface once a year to clear up the UV degradation.
Oh, and keep a plastic-lined bucket near at hand while doing clean up with paper towels. You *will* need it.
Style and appropriateness for your particular boat design was not mentioned... some boats look fine with this modification. Others look, well, um, not so good. Consider carefully, before you choose to go frameless. Remember the fellow in the Indy Jones movie that chose the wrong goblet... "He chose... poorly," said the ancient knight...
Good Luck.