There are no long term data yet. By the time there are, the E46 M3 wil not be a desirable car to turbocharge.
My opinion is that the HPF kit is a great option. The worse thing that can happen is you pop and engine. The cost of a rebuild (you would then have the option to rebuild with low compression pistons ie HPF Stage 3) would still be a lot cheaper than selling and buying a new GTR.