This is not considered a bad idea if you are a little careful about this and know the consequences.
You just need to make sure that you are comparing the old version with the new version of the standard template (i.e. when upgrading from Plone 3.3 to 4.0) and update your own main_template accordingly.
Between major versions, main_template may change, and you want your custom version to have the same features.
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