Tom-Yes you can do that as far as I can tell. I wonder why you want to go with 0.06 rather than the same thickness as the actual skin-which is what the GCR advises. I have not seen any car with the bondo done, but would think it OK if you do not disturb the inner structure. In my case my fabricator took the skin off and replaced it with a DX panel (yes they are still available)
Just my experience.

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'89 CRX Si-SCCA ITA
'96 Civic HB Just cruising daily
'99 Prelude=a sweet song in motion