I would strongly suggest boiling the lentils first and then adding them to the bake or to the semi-finished product.
Keep in mind that when baking at 325 F lentils may easily take 30-60 minutes.
Adding the lentils separately, once cooked, will let you control the flavour and texture of the respective dishes as well. For example let’s say you were to bake for 60 minutes to ensure the lentils are cooked. However your other meal ends up possibly over cooked, and it could easily ruin the meal’s nutritional content and unique textures, especially for denatured protein such as chicken or pork.
Regardless of cooking via stovetop or in the oven it will be critical to know what type of lentil; different varieties can range from 30 minutes at 325 for red lentils to as much as 60 minutes or more in cook time for brown lentils.
If you’re mixing everything in the stove it’s hard to control water content
Lentils absorb water quickly when cooking, up to 100% of their volume in water. If you’re just throwing them into a low-moisture dish in the oven they may not cook at all, and trust me, it’ll back you up if you eat uncooked lentils.