So an X5R capacitor should have the same 0.1uF 5% rating throughout the -55C to 85C range
Uhhh... not even close. The capacitance of a ceramic capacitor varies widely in operation. The "R" in X5R/X7R means +- 15% over the temperature range, so you could be 20% out on a supposedly "5% tolerance" capacitor.
And that is just temperature. You also need to take applied voltage into account. Depending on the DC bias applied on a ceramic capacitor they can sometimes be only a tiny fraction of the marked capacitance. You need to choose very carefully, taking all aspects of your application into account.
... but exceeding this is fine during shipment and assembly, correct? The reduced maximum temperature rating of 125C on an X7R is only gained when the device is turned on. Correct? Excessive heat during assembly, rework, or shipment shouldn't be an issue?
You need to look at the datasheet for storage vs. operating parameters.
Some of the capacitor companies' websites have tools to investigate environmental factors, etc. more closely and compare various parts. Murata and TDK do for sure, many others likely have some kind of comparison tool so you don't need to study a gazillion datasheets just to narrow down your search.
Beware the ceramic capacitor boogeyman!