You can microwave freezer bags, they are rated for that and yes, the manufacturers do test for that use (read the boxes or go to their websites).

The water used for FBC meals is at or lower than if you were heating foods in your microwave. (Steam gets quite hot, very fast)

As GH points out, you are NOT cooking, you are using hot (NOT boiling) water to rehydrate.

More so, polyethylene is a food grade plastic designed for levels of heat and cold. It does not contain BPA or any of the other items people worry about. Poly is used in most shelf stable bags of food, such as bags of precooked rice that one can simmer or microwave. Also seen in Food Vac bags.....

You can of course use your pot. Nothing stops you from that.