Hi Adrian,
It does work, but it's difficult to 
say more than this since you're conflating several issues. Firstly, you 
ask if a Tycho project can follow default Maven structure, but then
 suddenly jump to ask if PDE supports default Maven structure. Secondly,
 the error you mention is about location of class files, but you for 
some reason ask about location of source files too. Thirdly, there is no
 magic about "self-hosting". It's like hosting in any other p2 
application but using own p2 repos. All of this is confusing me.
If
 I were you, I'd try couple things. First of all, build.properties I've 
seen so far always included a dot (".") in bin.includes. I haven't 
reflected about this but think it's suspiciout that the dot is missing 
in your case. Secondly, I suggest that you export your product and 
inspect offending jar file manually. Does it really have classes? Where 
are they?
My theory is PDE indeed has built-in support
 for classes in bin/ directory but if they end up elsewhere bin.includes
 should include (heh?) the path to them.
Kind regards,
Mikhail Kalkov