I agree. I'm the opposite: a very experienced embedded developer but relatively new to web development (though my BBB is currently serving up a page monitoring my mechanical room).
It's like pulling teeth to find out any but the most basic specs of the BBB. I haven't used it much because a lot of what I wanted to do would have required so much experimentation to figure out stuff that should already have been documented. I just don't have that kind of time these days.
It's been a while since I looked at it. IIRC, the main problem I had was that many of the IO lines had shared/multiple functions and I couldn't find any documentation that explained how to switch them.
e.g. (contrived example), if a bit was MOSI for an SPI interface or DIO on port C, I had no idea which one it defaulted to and how to use it for the alternate function.
I got it to work for basic I/O, but it's obviously capable of much more.
It's like pulling teeth to find out any but the most basic specs of the BBB. I haven't used it much because a lot of what I wanted to do would have required so much experimentation to figure out stuff that should already have been documented. I just don't have that kind of time these days.