Marble and even faux stone countertops are usually pretty flat, flat enough for what you are doing. Generally, thick pieces of MDF also give a very flat surface for most purposes. EDIT: But nothing is more appropriate to use for checking the cover than the cylinder head itself.
If it is one corner that is up, you may find it is due to twist that you need to work out of the cover by clamping one edge down and then clamping a lever to the flange to twist it the "other way". If you RTV the gasket to the valve cover you can easily accommodate 0.010" or more waviness.
To compensate for the gaps, clean all gasket residue off the head and the seal track on the valve cover then degrease both.
Spread a thin coat of grease on the top of the cylinder head where the gasket will sit, then press the new gasket firmly down against the head.
Apply RTV to the gasket track on the valve cover, a thin continuous bead.
Lower the valve cover onto the gasket and tighten the hardware finger tight to hold the cover down in place.
Allow over night for the RTV to cure, then tighten the cover completely.
The grease will hold the new gasket down flat against the head and provide a release when taking the valve cover off.
The RTV will both bond the gasket to the cover and fill all the waviness and voids to the valve cover seal track.
It takes a bit more time to do it this way but it provides an excellent seal, requires very low torque to achieve a seal, and the valve cover is removable multiple times for service.