" ... I tend to create my extrusion shapes by boolean'ing together a series of 2D shapes first"

I've had good luck building smooth 2D profile closed curves by drawing the critical segments first, then use Blends to bridge the gaps. That is, use Blend to create the radius transitions to complete the closed curve.

This has given me no problems when it comes time to extrude and fillet the resulting solid.

Perhaps Michael can chime in and explain if a Blend on two line segments will always be tangent where they join.

I may be drawing curves in a more complex way than necessary, but I find Blend works well for 2D drawings.

Click image to enlarge.

Ed