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Will giving layers the same name in the ArcMap TOC impact analysis or give unexpected results?
Yes. Giving layers the same name makes it ambiguous as to which layer is used by the geoprocessing tools.
Consider the following situation in which both layers have the same name but one layer is a point layer while the other layer is a polygon layer. Buffer is run at the command prompt and the dynamic dropdown list, circled in red, is used to select the second layer named 'Reedley' as the input.
Expect the tool to buffer the polygons because that layer is second in the ArcMap table of contents. However, the resulting feature class shows that the points have actually been buffered, not the polygons.
Internally, ArcMap reads the table of contents entries from bottom to top, so first choice in the command line dropdown is the last entry in the TOC. To prevent ambiguity avoid giving layers the same name.