Great thread and very helpful chart. But what if your project is intended for CD?
You should still follow the chart.
Is the "cost" of sample rate conversion worth the additional quality of using a higher sample rate?
It depends, but theoretically, yes. If you record multiple analog sources at 48 kHz, process and bounce to a stereo 48 kHz file you will have benefited from the higher sample rate on multiple channels, but only had to live with one stage of (hopefully high quality) sample rate conversion.
If yes, which one yields the cleanest down conversion to 44.1? What do you recommend in this case?
Izotope RX gives you the best quality and most flexible parameters.
However, I recommend you stay at the original sample rate (e.g. 48 kHz) and let your mastering engineer perform mastering at the original rate. Then let him convert to your destination rate, e.g. 44.1 kHz.
If you perform DIY mastering be wary of inter-sample peaks on SRC'ed clipped or limited materia, and leave some extra headroom.