I think the usage of Lens flare/other filters greatly depends on the picture, and most of all - the painting style. In general I would say - If you want a lens flare effect, better paint it by hand.
I personally am against the Photoshop Lens Flare as it more often than not ends up looking rather cheap/artificial.As any computer-generated effect, Lens flare is just too technical for most styles. If the painting is cartoonish, or even realistic but with loose, visible brushstrokes, the filter might simply end up looking "pasted in" and thus cheap. It's kind of like painting a square - if you use a photoshop generated
auto-form and compose it with other hand painted forms, it will look too
"techncially perfect" to match.
Sure, lens flare among other auto filters can sometimes greatly enhance the final effect, but this has to be done with extra caution. I personally prefer to use the generated version as a reference to painting my own version imperfectly by hand... However, there are too many factors to give out a universal opinion.