Using tube amp upside down

I have a DIYish stereo tube amp that has the common tube amp layout: output and power transformers along the back row of a metal top plate, and quad of EL34s in front, and point to point components underneath.  The sides and bottom of the amp are essentially a wooden box, similar to Bottlehead amps.

I found that my amp sounds much better when placed upside down, resting directly on the output transformers.  I am assuming that when using the amp right side up, the wood sides and bottom that the amp rests on are adding resonance that does not gel well with my system.  Various decoupling footers and cones that I tried do help, but turning the amp upside down removes all this from the equation and sounds the best.

I am supporting the transformers with cones which also allows plenty of breathing room under and around the amp.  Is there any harm in running an amp like this?  I recall that some guitar amps have their tubes mounted upside down, but I have never seen a hifi amp with this configuration.  They always have the tubes sideways or right side up.

Sure, it will work that way but one of the main problems would be with lack of heat dissipation. 
Instead of the power tubes radiating upwards to free air in the normal position, they will now be funneling the heat to the base, socket and chassis top. This can place undue heat stress on both the tubes and other associated components.
Perhaps you may want to try a different way to couple the base to you're table/stand. I installed spikes in the wood side panels on an amp of similar construction with great success. 
The bottom plate may not be of sufficient rigidity to properly transmit the energy down and out.
This is where I would start. 
Fix the problem.
Does the music come out upside down? LOL
Maybe you are dissipating transformer induced vibration from chassis when using amp upside down. You might try dampening the transformers another way. 
I've seen lots of tube guitar amps with tubes upside down. Definitely due to the sound benefit.
Thanks for the suggestion jadedavid.  I experimented further and ditched the bottom panel completely, using Audio Points to drain the energy out directly from the side panels.  This was a huge step in the right direction!  I may think about threading the Audio Points into the side panels later to see if that helps but for now will try to find more ways to more efficiently "ground" the amp.