Can I ask why? I assume you know that no quality is lost in conversions between lossless and uncompressed WAV/AIFF/PCM.
That's not possible. Track boundaries won't match FLAC frame boundaries, so the first frame of the second track will have to be shorter than the rest, and FLAC subset doesn't allow variable frame sizes.
In FLAC, as in most lossless codecs, only the last frame is allowed to be shorter than the rest. All other frames usually have default size of 4096 or 4608 samples. Why does transcoding bother you? Lossless transcoding is not exactly a transcoding, because every bit of information is preserved. And with FLAC it can be very fast, even faster than splitting a WAV, because there'll be less work for HDD.