Yes, you've gotten the picture.
You get a hard drive for your PC - some large part of that gets sucked up by the operating system and any pre-installed goodies. You don't get to use the whole hard drive space for your apps and data.
Internal storage on these phones is acting like the hard drive on your PC.
And add in your PC has some BIOS chips in it that configure things and get it to boot.
In the case of the Evo or 3vo or Shift or ... that's all fitting that - and the radio firmware - into the space called internal storage (aka ROM on some spec sheets).
And if any apps insist on putting their data and cache into that space rather than the SD card, that'll eat that internal storage up doing that, too.
Some accept this, some don't and want to have free memory spec'd. HTC simply says space available to the user will depend on software configuration (of the pre-installed stuff).
This is why moving apps to the SD card was so important. Not a perfect solution, but a pretty good one.