I've addressed similar concerns in the past, but I'll give the best answer I can.
The ero manga industry isn't much different from any other form of media. Hollywood and AAA developers tend to stick to what's safe (which typically means sequels and reboots of popular series), while the independent scene is where they innovate and create things for the niche market. It all comes down to money and risks; a multi-billion dollar movie with thousands of staff can't afford to fail, whereas the hobbyist does it as a passion project.
It's the same deal with ero manga. Commercial manga (magazines and books) sticks to content with broad appeal, while the indie scene (doujinshi) is where artists are free to experiment with odd fetishes. There are certain doujin circles that focus on a unique fetish that no one else does, and this works because they can minimize loss (or possible turn a profit) by selling to a couple hundred customers who are interested in that genre. On the other hand, it wouldn't work if you put the same content in a major magazine that goes out to millions of readers, due to the risk of alienating the 99.9% of their audience who doesn't care for that material. When a doujinshi flops, one artist has to take the loss. When a magazine flops, an entire publishing company and potentially hundreds of artists are affected.
A common suggestion that's brought up in this discussions is Comic Unreal. Looking at recent issues, it seems futanari is present in every other issue. Assuming it's a single chapter, this means that futanari only makes up 2-3% of their content, despite being one of the most prominent sources of "alternative" material. I imagine this is a similar situation as with
Comic Bavel, which has a
single artist who specializes in monster girl content. This is pretty unusual mind you, because typically when an amateur who does alternative stuff get published, they shift to drawing more "normal" material for the magazine.
To sum it all up, we could pick up every major commercial magazine currently released in Japan, and the ratio between mainstream and alternative content would stay mostly unchanged. As I've said before, doujinshi is always going to be where you'll find the more extreme or unusual fetishes. In some rare cases, a prolific doujinshi artist may land a book deal, which was the case for
Futabu! Mix, but it's so rare it was even addressed in the afterword of the book:
This probably wasn't exactly the answer you were hoping for, but I hope it at least helped explain why things are the way they are. Also...
Gadien wrote...
Additionally is there a way to see the free to read while subscribed and not see the books?
To my knowledge, the best way to do this would be to exclude the Book and Doujin tag from your searches. For instance "futanari -doujin"