Heating Wooden Vivarium

I would agree with cutting the hole for the heat mat then plexiglass over the top... it would suck to have to make alterations to a new viv but at least this is a solution to your problem. Also, if the heat mat or prob ever failed you could easily replace them. Save the wood that's removed and you could put it back with wood glue later, but you would have to keep the plexiglass to keep it sealed.
Or...
You could place the heat mat on top of the wood (on the inside) then some kind of spacers for the area where the heat mat isn't then place your plexiglass (or tile) over that. Just keep in mind that these items do fail and you'll have to be able to replace them without too much work.
Hope this helps and please share photos once you have everything set up. :)

Use a router and cut out a hole just slightly deeper than the height of the tile and heat mat) and 1/2" bigger in each direction around the perimeter of the size of the tile.

Place your heat mat in that pocket you've created and run a bead of silicone around the peremeter of the opening then carfully set your tile(or plexi if you'd like) into the pocket pressing gently until the surface of the tile/plexi is flush with the height of the floor of the enclosure. Caulk around the 1/4" gap with silicone and wipe away excess and smooth with a silicone squeegee or a wet finger until the transition is smooth.

After it has dried and fully cured, hot glue the probe down on top of the tile/plexi and set t-stat until desired hot spot temp is achieved (may need to have higher t-stat reading to achieve target temp) and make sure temps stay stable for a few days.

And you're done.

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