I’m talking about the floating transport, NOT the bottom transport bar.
Upon researching this I can see it’s been a problem for a long time, and it happens to me every time I open up Cubase for the first time. It also happened in C8.5. It’s not the end of the world but seems like a very long overdue fix. Do others experience this, too?
Not sure I understand. You want the floating transport to be always shown when you open Cubase? Hitting F2 is an annoyance?
Or is it that it is buried behind another window so you can’t get it up? If that is the case then there is an issue. I do not have that myself.
My floating transport panel opened every time I started Cubase (not any more as I now use the lower transport in CB9). But, I suggest that you look at the Cubase>Preferences>General menu and change the setting for “Open project in last view used” to “Always”. By selecting “Always” Cubase will always open in the last view saved before closing. So if saved with the floating transport panel showing, Cubase will open with it showing. Be aware that this setting does not mean that every separate project will open the way they were saved. It means they will open the way the last one was saved.
Weird wild stuff for sure as it relates to opening projects but… at least the transport will be open if it was open during the last save. What the??? 
Regards. 