"ACA seems to have made the routes straight line rather than "auto" which seems to mean following roads that curve.
"Is there any way to convert them?"
All you have to do is select the route (and you may be able to select them all at once) and tell your software to recalculate the route. It will do that according to whatever preferences you have set -- e.g. shortest, quickest, etc. It will know which waypoints to use. However, your software probably doesn't show, or follow, bike trails. Instead, where the ACA waypoints are on bike trails, your software will construct a convoluted road route that hits all the waypoints, but makes no sense. A good example is the very first route out of Anacortes on the Northern Tier. If you check the comments of the waypoints that seem to be problematic, you'll see that they refer to bike trails. I have no solution for that.