it may well be a fundamental 68k problem, or an exec issue. amiga and atari machines werent built with huge multiple megabytes binaries in mind, frequently allocating and deallocating small bits of memeory. i mean to have observed similar issues when for instance trying to compile something larger with cubic ide. with ixemul the problem likely has been masked by using its own linux memory allocation mechanism. on faster machines or uae the inefficiency might be masked by the pure computing power, or jit, even though os4, aros and morphos exec may differ from the genuine one in this respect.
some general profiling would be neccessary, based on a simple testcase, which may result in need to rewrite parts of the system itself to get rid of this bottleneck.