Varnishes, even matt ones, tend to tone down the effect of weathering powders. I have a theory that this is because part of the effect of weathering is due to the fine powder having a different reflectivity than the surrounding paint which we perceive as part of the weathering. If you seal with a varnish, this part of the weathering effect is lost as the whole area is returned to a uniform level of reflectivity.
One solution is to over-apply the powder initially in the expectation that the sealing will tone it down. This is where some cheap wagons from the bargain bins at model shows make great fodder for practice before you apply your skills to the latest RTR offerings.
I have heard that some people seal very successfully with cheap unscented hairspray although I have not tried this myself. My worry about leaving the weathering unsealed is that handling would cause it to wear off over time.