if I compile with Qt/X11 I need to start it from X server (otherwise it doesn't run).
if I compile with Qt/Embedded I need to start it from the prompt (otherwise it doesn't run).
It depends on what application you want to run: if it's really just one application with low graphics output, the Qt/Embedded will also work, but you'll need to compile Qt for TinyCore yourself and can't use the libs from the AppBrowser.
I've hacked together a box running the audio player "Partyman" on a mini-itx N270 board. During this I was faced with the same question: should I use Qt/Embedded with framebuffer, or Qt/X11? My choice was going the X11 way. It saved me a lot of unnecessary work.
Qt/Embedded with framebuffer is very interesting if you've got hardware that's limited in space, both ram and/or mass-storage (usually flash in that context), but I've you're using an itx-board, you've got at least 256MB up to a range of 2GB of RAM and boot from an old HD or a CF card. These come with storage capacity where the space for Xorg really doesn't matter.
Concentrate on your project, not the platform! Get your work done, not the work that's already done.