The obvious canonical examples would have to be lex and yacc. They generate .c and .h files into the blddir, and automake has built-in mechanisms to include the generated sources into the tarball.
No argument there, but vala is so much newer than lex and yacc, especially in terms of Automake support. I don't see the need to create in these latter days yet another special case for treating intermediate files non-intermediately. Reuben's option 1 seems simplest to me: just treat the vala intermediate files as intermediate. Not in make dist. Jim/Paul/anyone, wdyt?