Simon, you always seem to get these weird design jobs with very tight constraints...
The best way is definitely to heat the product if you need to go to -46, you'll really struggle to get components rated for that temperature (you'll need -50 to build in margin) in realistic quantity, at realistic prices and with realistic lead-times.
(Not only that, but you'll really need to take into account the coefficient of thermal expansion of the potting compound if you need the product to work over a very wide temperature range. I make potted stuff that is spec'd from -40 to 70C, and it ain't easy to get right.)
In fact, it's *easier* to heat because it's potted, you can maintain the resin relatively isothermal because the resin is an excellent thermal conductor, rather than relying on heating air in a normal enclosure. The simplest way to do it would be to use some low value resistors dotted around the perimeter of the PCB. When the temperature gets below, say, -10, use a spare pin on your MCU to PWM the resistors (via a mosfet) to begin heating the resin. As the temperature drops, increase the duty cycle to maintain a relatively constant temperature within 10-20 degrees or so. Use any old temperature sensor you like, it doesn't need to be particularly accurate. MCP9700 series springs to mind.
If you have a voltage regulator in there dissipating enough power that you need to worry about it at 50C ambient, then you probably have enough heating as it is anyway.