First off, we aren't currently talking about what an ideal air circulation system might be, we're just choosing between the two options you listed. There of course can be some better setups depending on what resources are available and what your priorities are.
The general reason to put components before the fan is because centrifugal fans pull better than they push. The more restrictive the filter is, the greater the impact of certain problems becomes, most from imperfections found in every system, until the drawbacks outweigh the benefits.
The more freely air flows, the less change in pressure there is, and vise versa. The more restrictive the filter is, the greater the vacuum between the filter media and the fan, up to the maximum vacuum the fan can generate. The more components, joints, etc. between the filter & fan, the more tiny leaks there are likely to be. The higher the vacuum, the more CFM is lost in a leak and the greater the chance new leaks will form. Aside from leaks, any pathway the vacuum is inside of can deform (bend inward), which absorbs some of the energy. Also, the more area between the fan & filter, the less suction actually gets to the filter.
Nearly all of these are irrelevant if the filter isn't restrictive enough to increase vacuum, where the benefits of having components before the fan come back into play.