dross56,
If you are talking about the pump suction and discharge flanges, the answer is yes. Any significant out of alignment between the pump and piping flanges will be reflected in misalignment of the shaft. The greater the flange loads, the more misalignment. API 610 provides allowable flange loads. Even these limits result in seal misalignment which as I recall is limited (by API 610) to about 0.002" with maximum flange loads.
If you are referring to upstream and downstream flanges, the same maximum allowable flange loadings (at the pump flange) will also apply.