Whatever will sound best in a given musical circumstance and with your particular setup is what you should use. It may or may not mean using standard trill fingerings, but if you have a way to improve tone or intonation, then I say use it! What matters most is not whether or not you do the conventional thing, but that you provide the most pleasurable listening experience possible to the audience! I have one suggestion....Have you tried doing the trill with LH1 leaked very slightly? At least on my flutes it seems provide a good compromise tone-wise.
On this trill I usually start with the correct fingering and half open the LH index finger until it sounds good. Play the trill and experiment on controlling lifting your index finger just enough to get a good sound. It'll will take some practice, but your d-e trill will be like riding a bike once you get used to it.
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