Drop in filters are usual used because the front element is too larger where it would be too expensive or impossible to attach a filter. Because the filter is in the lens, they become an optical component and so the lens is always supplied with an optical blank--a piece of glass needs to be in that position.
Neither type of filter should be in a position that has "focused" light. You do not want defects or dirt impacting the image. An internal filter is near the aperture for that reason and a front filter is within the focal length.
The internal filter can have an advantage of being in the space the aperture occupies as the light is in a sense collimated. A front filter on a wide will have a longer optical path length for off-axis light.
But I don't think the filter position is that important as far as quality--I doubt you would ever be able to see the difference. However, the quality of the filter is important.http://www.lenstip.com/113.1-article-UV_filters_test.html