There appears to be some inconsistency or precision issues with scene depth and stencil buffer depth values when using MSAA instead of FXAA/TAA.
For example, Tom Loomans post process outline material outlined here: Multi-color Outline Post Process - Tom Looman
Will work as intended with TAA or FXAA, however has edge cases where the depth comparison between the Scene Depth node and the Custom/Stencil depth (for occlusion detection) is slightly different on thin geometry or edges (seems like precision issues) counting visible pixels as occluded in the check.
Also a simple post process that renders a flat color instead of scene texture of objects in the custom depth buffer that are occluded will show artifacts with MSAA on thin geometry and at edges but will be clean with the other AA options.
I am unaware of if this is an expected issue with MSAA because of how it re-samples the scene but figured I should bring it up.