Unfortunately no, I just managed to get iframe to work without the browser alerts :(
My first published game on Itch.io is a desktop release so i didn't have problems with file count. At first I did try to upload html5 browser version here and on Game Jolt but both sites had some problems with the video plugin I was using so I decided to publish desktop versions. The only fully functioning htlm5 browser version was published on Newgrounds.
For my new game I have decided not to go with desktop versions, different video plugin worked out great but I'm stuck with over 300 files. The game test-zip is functioning on Newgrounds and Game Jolt but here it has problems (error messages) that I think can only be attributed to the file count.
I don't know why there is a 100 files limit on Itch.io, I'm sure it's there for a reason. I could try packing the files with some sort of software that Construct 2 engine could read from during the gameplay but I guess iframe is more practical solution.