So I'm pretty sure others have noticed this bug but Ill explain it and hopefully it gets fixed. So when you customize a car and you save it in a garage it has its times were it will stay there next game session however other times it's gone and it's not in the impound lot. Cars also disappears after you buy the garage and your left outside with no car and they may or may not be in the impound lot I didn't check. Another thing about the impound lot that I believe is a problem is that the game impounds your vehicle after a mission and it's quite an inconvenience it should be sent back to the garage at least. Also I have had cars impounded when they were parked properly and not abandoned. In conclusion, cars have an issue saving so customizing or even buy them is pointless.
I'm sure Rockstar willl address this. The only vehicles which stay saved are planes, helicopters, and the Rhino (i've destroyed them and they were still in the hanger). Also the "signature" vehicles owned by each character will retain their upgrades (ie. if you upgrade Franklin's white car it will stay that way even if it's destroyed).