Not if the docking transport is an Elysium, and the extra minute it takes to get in to position and traverse the longer docking path may affect the way the mission plays out. The dockpaths were done with certain ships in mind, and so have particular characteristics that limit their functionality in a general sense but allow those smaller ships to dock more easily. You wouldn't expect a Hippocrates to dock sanely with anything, would you? It's a timing thing rather than a graphics thing, an important factor in mission balancing that people often forget.
If it's a problem, add another dockpoint or two for argos. But you can't alter the ones that are there for reasons previously stated. If the paths were backwards, or the docking point inverted, or something else obviously stupid (see Iceni) then you'd have a case for changing the existing ones, but that doesn't apply to those with paths that are just too short for the cruiser-sized Argo transport.
That also doesn't address the backwardsness issue, but the reason that can't be changed should be more obvious.
And turret changes are a little different (particularly with the Aeolus) because the change made was actually purely cosmetic. Those firepoints already had huge firing cones IIRC, so making it true multipart only made it actually turn like it was supposed to.