Interesting point of distinction.

Irrespective of how you define the principle of charity (i.e. motivation based or intelligence based), I do believe that the principle on the whole should not become a universal guideline and it is important to distinguish it, a sort of "principle of differential charity". This is obviously similar to basic real world things (eg. expertise when it comes to the intelligent charity issue and/or political/official positioning when it comes to the motivation issue).

I also realise that being differentially charitable may come with the risk of becoming even more biased, if you're priors themselves are based on extremely biased findings. However, I would think that by and large it works well, and is a great time saver when deciding how much effort to put into evaluating claims and statements alike.