If you think about what your goals are with conformal coating, then you can look at alternative solutions. You are trying to protect a solder joint in your case from moisture. If moisture condenses on the solder joint you can start to have adverse effects such a dendrite growth.
By covering the solder joint with a polymer you are providing a barrier to moisture. Other materials such as encapsulants can provide similar protection. The problem is that you have to start to think about what is in the fluid you are now going to use in place of the conformal coating. Is the encapsulant clean or does it have any chlorine in it as a number of low cost epoxies do.
Remember that this work has been done for you by the conformal coating manufacturer.
Similarly if you try to use an epoxy preform, how does it wet to the solder joint.Does it flow well over the jointand not have any inclusions where moisture can coalesce?
In the end it may be easier to use conformal coating because some of the work has been done for you. The trick may be to use a selective coating system that is easy to use and program to minimize the work load on your operators.