Simon, just go for it. We pot almost all our products one way or another in PX700K epoxy from Robnor. It's very thermally conductive and we regularly pot components dissipating a few watts (we do ensure there's lot of copper fill on the PCB to spread the heat, it's important to avoid hotspots). We heat the unmixed epoxy to 50 degrees to reduce its viscosity prior to mixing, and owing to its low exothermicity and 24h cure time it does not seem to cause any component stress whatsoever.
Coefficient of thermal expansion has never been an issue for us, we regularly pot 0603 passives, QFPs and QFNs on standard FR4 with no problems of components being ripped off whatsoever. It's far more thermally conductive than air, even free-circulating air, unbeatable for ingress protection, and great for protecting against tin whisker growth, vibration damage and even arc-flashover. We've never had EMC problems using it either.
We ensure component temperature is limited to less than 70 degrees in the resin under worst case conditions (if we're not sure we'll pot an LM35 or a thermocouple right at the component in question to test it). The 3-yr failure rate on our potted products is less than 0.1%.
We use the 1kg twinpacks of the PX700K resin, it's cheaper for me to employ somebody to fill the products by hand than it is to buy and maintain the dispensing machine from Robnor. We cure under an IR lamp at about 30 degrees for 24 hours. I suspect problems occur if you try to cure faster.
We make a lot of IP rated stuff and stuff for marine environments, and potting is indispensible. In fact I try to use it as much as possible. It's costly and labour intensive, but the benefits are numerous in all respects. I don't see what all the fuss is about....