Even when you do a coincident mate it flips them the wrong way. It doesn't make sense, I've just learned to live with it.
While the bolt is still on the mouse and in preview graphics (as shown below), simply press the Tab key to flip it's orientation.
We've been doing the Tab thing for as long as I can remember. It boggles my mind that it is even necessary. Can you tell us if there are plans to fix it so that by default this is not necessary? If it is not possible to fix it can you explain why? I'm more curious than miffed.
It's odd, on my machine using 2017 it comes in with the proper orientation but in 2016 it comes in reversed. There is an SPR open for it but it only has a few hits on it over the last 6 releases. If you're still seeing it, please vote for it.
SPR 625323: Toolbox parts inserted into countersunk holes are always incorrectly aligned by auto mates, TAB required to fix
Use a right-hand screw thread (just kidding).
I doubt if this is the case in your situation, but I had a bolt that would always come in upside down also. I finally sent it to my VAR and they discovered that the head and shaft were two separate bodies. When I edited the Part to combine them the problem went away. Again, that may not be the situation in your case, but I thought I'd mention it anyway.
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