The goal is efficient extraction, and it can be measured in two ways: the end temperature is approximately 160 F, or a certain amount of energy measured in watts per second has been absorbed into your mixture.† It doesn't matter how you go about determining the energy used, as long as it points to the same result.† Measuring the end temperature is just one way of determining the energy absorbed, and probably the most convenient for you.† For example, because of how a microwave oven works, you won't register a very high temperature if you don't add enough water (as you've seen) since the source of the thermal energy is the water itself, converted from the microwaves.† The solution: add more water in the beginning until the end temperature reaches 160 F.† It's not the end of the world if you add a little too much water.† All you'll end up with is more water in the end.† If you add way too much water, which I doubt you're doing, you won't extract a high percentage from the seasonings.† It's also not a big deal if the end temperature is over 160 F, as this is a sign you've extracted all you can within reason, but you deal with the evaporation of some resins which would have otherwise provided flavor.
There isn't a lot of "flavor" locked up in the cell structure of tomatoes.† How you warm your tomato sauce isn't critical at all.† I am curious why you're heating the sauce though.† Is it for dipping breadsticks or something like that?† If not for using as a side sauce, I wouldn't heat up the sauce for anything.† That's one of the main reasons for using MAE on the seasonings in the first place.
The following abstract is from University of California's Department of Food Science and Technology Journal of Food Processing and Preservation (2002):
"During the dehydration of onion and garlic products, use of high temperatures is undesirable due to the potential loss of aroma and flavor characteristics. As a consequence, residual pectinesterase (PE) activity may be found in these dehydrated spices. This study reports the presence of PE activity in raw onions and in dehydrated onion and garlic products. Pectinesterase activity is higher in the raw onion stem disks, and dehydrated products made from this tissue, than in the bulbs. Dehydrated onion products induced gelation of citrus pectin solutions and tomato purees. Although some inactivation of PE in dehydrated onion water suspensions and extracts was observed after 10 min at 50C, complete inactivation required 2 min at 82C. Commercial dehydration operations may require reevaluation to eliminate residual PE activity in dehydrated onion and garlic products."
Yeah, it helps to have seasonings not older than six months.† Herbs and spices cost so little compared to the impact they make on our food.† I usually buy all new seasonings every couple of months whether I'm out or not, and I keep the older stuff for emergencies.