your experiment is very interesting & I believe that you may be pleasantly surprised by the results. I used a similar rack arrangement for many years & have always liked it. Not sure where your perception that MDF is undesirable came from, but I disagree with that conclusion based upon my own experience. I don't think that you'll need to treat the shelving at all. My shelves weren't even that thick: closer to 5/8" is all that mine were. And the whole thing was assembled from pieces in a Sauder Furniture kit; fastened with steel screws & the shelves sit on adjustable side pegs that plug into a column of holes such that the shelving heights are adjustable. Quite solid & rigid, it doesn't even have spikes which (I'm guessing) may not be very effective for this type of high mass rack anyway. Rather it has casters which are fantastic for rolling away from the wall & accessing the back of equipment for cabling changes or tweaks, but spikes could be installed in place of the casters (I have the spikes on hand, but I love the casters for convenience). It also had smoked glass doors which looked great, but I eventually removed them because I figured that it sounded a little better without them resonating, at least that was my perception. If you're interested in trying this rack it's now available cheap; it is shippable. I only replaced it because it has 7 shelves & I need 10 for my larger system now. It's double wide & even has compartment storage for records or accessories.
So I think that you'll have no problems with your new rack. You might find for certain pieces of equipment that audiophile shelving such as Black Diamond, Zoethecus, Symposium, Neuance, etc. placed atop the MDF shelves still enhances performance. Pods or cones placed between the MDF rack shelf & the audiophile equipment shelf sometimes enhances or even degrades sonics, or has no perceptible effect at all, so experimentation is required. Same applies for cones, footers, etc. placed between the components & the MDF shelf or the audiophile shelf when used. The whole thing responds quite well to these kinds of tweaks. My new larger rack is also made of wood, which I find much more attractive & WAF-friendly than black steel etc. Good luck with your project!
So I think that you'll have no problems with your new rack. You might find for certain pieces of equipment that audiophile shelving such as Black Diamond, Zoethecus, Symposium, Neuance, etc. placed atop the MDF shelves still enhances performance. Pods or cones placed between the MDF rack shelf & the audiophile equipment shelf sometimes enhances or even degrades sonics, or has no perceptible effect at all, so experimentation is required. Same applies for cones, footers, etc. placed between the components & the MDF shelf or the audiophile shelf when used. The whole thing responds quite well to these kinds of tweaks. My new larger rack is also made of wood, which I find much more attractive & WAF-friendly than black steel etc. Good luck with your project!