I haven't set up any tank without some sort of soft bedding between it and the stand for at least 40 years. My larger tanks are DIY plywood, and I have owned plenty of all-glass tanks as well, both framed and frameless, both commercial and home-made; full disclaimer, I have never owned an acrylic tank. For plywood and rimless glass I use a full-coverage rubber sheet; for a rimmed tank, my inherent cheapness has me cutting the sheet into narrow strips that are used to support only the edges where they make contact. I use the rubber for the exact reason you state, i.e. to cushion any slight imperfections or blips in the upper surface of the supporting structure. I still take pains to make sure the stand is level, the rubber isn't performing any function other than cushioning.
It's impossible to ask this question on MFK without being told that you're doing it wrong...regardless of which way you are doing it!
That rubber mat you linked to looks perfect; I'd use that in a heartbeat. Doesn't matter what width it comes in, just piece it together however way you can to get the full coverage support that acrylics apparently need. Doesn't matter if you have tiny gaps here and there between pieces, once the tank is in place that rubber won't be shifting around any.
Styrofoam works too, but it's a PITA to get it in place, trimming the edges is messy, it looks like crap, it's easily damaged...give me a black rubber pad every time!
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