It's not that the program doesn't start correctly..... The primary reason for not opening from an explorer window is so that Revit can create a local file instead of opening the central file directly. Opening the Central file directly and working away can cause a lot of people to be very upset with whoever does it. Same goes for the "Recent Files" splash page.....don't use it!

The person I heard about it not starting correctly was a Revit instructor during a training session a while back. He may have been gassing us up... But I think it may also have some validity. I will have to bounce it off of a CS buddy. Yes.. that was another reason I told everyone I work with to never ever ever use the splash page. And always make sure the "create new local" is selected. If anything make a shortcut in the open window... We had an issue with someone working in the central file recently which is why I brought this up..

People like opening their local file too....even from explorer....then when they cannot sync they blame Revit instead of their foolishness...

I'm not sure if this is the case with Revit, but with AutoCAD, there are "keys" that can be used in the shortcut that set things like which profile to use. A double click could bypass the shortcut and these "keys" opening from the .exe in the program directory rather than the shortcut with the "keys".

I don't know how many times I've posted this, but I've been advocating for years to just make the whole "Create a Local File" interface go away.
Not the process, just the interface. The way I'd like it to work is, once you've made a Central File, you simply open it. No check boxes, no "sometimes Central, sometimes Local", just ALWAYS make a Local file, and do it behind the scenes. The user should never see the Local File. It would still get created, but it would be hidden away in the Temp folder. Administrators would still need a back door to open a Central file directly, but the great unwashed masses should never have to worry about "Did I make a Local today?", "Can I open my Local?" "Do I need to SWC immediately?" and best of all, "Can I double-click on this rvt file?"

I think the process of having a Central file and a Local is a good solid concept. I just wish the user would never have to see it happening. Let them open a file just like they would with any other Windows application.

The Revit.exe file is the "same" file name regardless of version and flavor. If you double click on a file the version of Revit that opens will usually be the last version installed. That can be risky or at least tedious as Revit upgrades your Revit 2010 architecture file with Revit MEP 2015. You can change the File Association that Windows uses but how many people actually do that? How many know they can?

You may not have more than one flavor (Architecture, Structure or MEP) installed but it is still likely you'll have a couple of versions installed. I have 2012, 2013, 2014 and 2015 installed at the moment. The last thing I want to do is waste my time waiting for Revit to process an older file with a newer release.

Secondarily, as mentioned earlier, projects using worksets also don't want you to double click a file to ensure that you create a local file instead of opening the central file itself.

I guess it's from the days of "Copy central to C:\ to create a Local" and "Reboot your Pc at lunch time."
I remember Revit using the Ram a little bit better when you've opened a file through UI.