The only concern i would have is if you don’t connect the battery, and then plug in the USB cable into the Panda to power the system. The 5V power from the USB cable would back feed into pin2 of the TPS61200 IC. Though the block diagram shows it as a fet output, i have found that many times IC manuf, use generic block diagrams to help explain things when there is actually more in there.
Its best to play it safe.
To make it 100% safe, i would remove the series diode off the panda from the USB jack, so the USB cable cannot power the board. To power the board you would always use that external power supply.
you could go at it the way you explained, and put a series diode from the external power supply +5v to the panda +5v rail this way it would block any back feed.
Another big thing to check into is this, what is the min discharge voltage of the li-Po that you will be using. This is a pet peve of mine with Sparkfun concerning there li-po stuff. They do not tell people that many li-po’s cannot go below 3.2v. Draining a li-po below 3.2v is a VERY bad thing.
You MUST make sure that your battery can tolerate a discharge to that voltage.
it would be a good idea to solder the tabs of your cell to this for full protection both ways. I.E. charging and discharging.
Li-Po are great battery’s, but they are also the most sensitive to over charge and drain. If you have ever seen one catch fire you would understand my concern. They are violent when they catch on fire!!!
i had a 2200ma cell puff up and blow a 3’ intense flame out of it for ~8-12 seconds. Good thing i was in the garage when it started to puff up to throw it on the floor. I hate to think if i was not home and that happened.