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The javac shipped with Java RTS is from JDK 5.0u13 and so may not contain fixes from later versions of javac.
Otherwise the only difference is that the real-time VM has a different execution profile (in terms of performance and memory usage) to a regular VM, so a "real-time" javac may not be capable of compiling as many sources files together as the javac from the regular VM (at least not without tuning the RTGC :) ).
There is no difference in the code produced in either case.
"Cross-compiling" as you describe should not be a problem (at least there should not be any RT specific issues in cross-compiling). You need to be careful not to use any JDK 6+ API's as of course these won't be present in the JDK 5.0u13 runtime of Java RTS.