Tesla doesn't want you to get sick from the exhaust fumes.
<g>

Other than to close the boot lid or bypass the open sensor switch in the latch, I'm not aware of any way to turn off the notification. I'm also sure that if you brought that up to Engineering and asked for the option to disable that "feature" they'd get a really good laugh from it.

Alternately you could ping Elon directly on his new Tesla Official Communications Channel (TOCC) on twitter.

 

It seems to be just as much of a no brainer to leave the notification on. I'm not sure why it covers the turn by turn up though. You should be able to see them on the map or if the map is covered, at the bottom of the car graphics

 

...the warning stays on the instrument panel which means you lose the turn by turn navigation assistance.

I'm not sure which "turn by turn navigation assistance" you are referring to. But as Ed says, the location of the "next turn" instructions changes position on the display depending on whether the navigation map is currently active (in which case they appear at the corner of the map), or in the area with the car graphics (whenever some other screen is open & covering up the map). So try switching it to the "other" location when you're in that situation.