If the product is an oil like flow'able product then it will eventually migrate and coat the entire chain even if you wipe off the outside surfaces. That's why you had to re-wipe the chain.
Your option isn't that much different from my own of using a heavy body and low odor chain saw bar oil that I thin with a bit of mineral spirits. The only difference being that my lube is thin due to the solvent and not from microwaving. Thinning the product with a microwave does pretty much zero good since as soon as it hits the cold chain it'll thicken right up. You may want to try the mineral spirits option.
Thinning the product with solvent instead of warming it would also keep it thin long enough for you to apply enough to soak right through the chain to all the internals and for the product to stay thin enough for long enough to wipe off the excess far more easily and in far less time. And it'll avoid leaving greasy or oily finger marks on the controls of the microwave where you cook food.