Drew,
I would stay with small dots of Blu-tak, say less than 1/4" balls before the speakers' weight flattens them out. They will stick well enough to the Q-Stone marble of the Europa cabinet, but still release someday. Blu-tak does penetrate wood surfaces that are not sealed or painted, which should not be the case with your stands.
Your top-plate dimension is fine.
If your stands are well made, the vibration you feel is the floor itself moving. However, do make sure all four spikes (for carpet) or four feet (for wood or tile floors) are touching down. That can be a source of wiggle, and most easily checked for by pushing on the top plate of the speaker stand in a certain manner:
Push diagonally from corner to corner, only in the horizontal plane, parallel to the plane of the floor. Do not apply upwards or downwards pressures.
Hot spots in the midrange your meter will exaggerate. If they are audibly there on, say, female voices, then I would make a guess you need sidewall acoustic treatments. A photo of the setup would help anyone advise.
Good work on resolving your subwoofer issue! You received good advice from everyone. That remaining 10dB rise in the low bass is half room-caused and half from the subwoofer's design, from its too-small box size and likely some built-in low-bass EQ. Do not add extra stuffing to that box.
Instead, use your ears to determine if that measured bass rise is audibly OK, probably tested listening to string bass, because the Fletcher-Munson curve is somewhat applicable to what you 'need to hear.'
Feel free to contact me directly. I would appreciate knowing your results.
Best regards,
Roy Johnson
Designer
Green Mountain Audio