I'm just trying to envision your project. A more detailed description would be helpful. Generally in multiple mortise situations, you'll need to make a surety (holding) jig to guide long stock. If the tenon is part of the stock that the mortise is to accept, and there are several, absolute identical mortises have to be cut. The possibility of one or more being slightly off will disrupt the fitting of the others. An example that's easy to understand is a handrail and balusters. If multiple mortises are the plan, for the mortiser, make a jig to slide the stock and hold it perfectly. It's important to create in your jig a clamping method that locks the stock in the correct position before machining.
To mortise with a plunge router, a running jig, like rails to hold the stock, with the ability to move the router to position on top of the rails, and guides to position the router so the stock and the router don't move. It would be like a channel that the router sits on with the stock inside. It sounds like a lot of trouble, and maybe it is. Doing it right, only one time is what you should be after.
An alternative I've used is to use dowels as a loose tenon. Depending on the size of the pieces, if you think about it once the dowel is in one piece it becomes technically a tenon. Sometimes it is easier to drill holes or use a forstner bit in a drill press. But still in any case you should make a guide jig to hold the work.
