Hi,
I have a Pearl SBX with 12x9, similar enough maybe I can help. I've tried EC2 over G1 and am currently using G2 coated over G1.
I don't think there's anything wrong with your tuning technique. Your batter and resonant heads are both making a pretty clean tone (G#) and are matched. The overall tom tone is a B which I think is in the good tuning range for that tom. (I don't have a good ear, by the way, I just run a spectrum analyzer on the tail of your samples as I do sometimes on recordings of my own kits.)
If you're hearing a buzz, my experience with my kit has been that the G1's don't seat well in low tension (and there is a little bit of a close harmonic in your resonant tom waveform that often comes from that). They don't seat on the head tightly all around. I haven't found a detectable problem with the kit construction, but I often find that there's a little looseness between a couple lugs even when a drum dial says the head is evenly tensioned. Resting your finger around the drum head edge while you play will help you find it. Rather than tune the whole drum up, I break the rules a bit and just tune up a couple lugs a hair and it actually sounds better.
Now, on the whole "thinness" of the kit sound, for one, realize of course you're not hitting that drum hard enough to get any pitch bend, so it will sound a bit jazzy even in low tuning.
And secondly, I've never been inspired with the sound of my birch kit in a small room at any tuning. It sounds outstanding projecting in a club or outdoors but in my house I much prefer the tone I get out of my cheapo Luan kit to be honest. When I take it over to my friends home studio, he close-mics it and it sounds good though.
Just my experience (and I'm far from an expert).