I think you did the right thing but in somewhat of the wrong way, in that you could have just said you needed to go to the bathroom and then sneaked the tip on the side.
On the other hand, even though it may have been rude towards your potential father in law, it's good that he was subtly shown that his entitled, arrogant petulance wasn't actually supported by all or ok, and that he was indeed being cheap. Sometimes people just need to be politely reminded of these things instead of having yes men and women around them all the time, and at least this incident would have acted as one of those low key reminders.
You don't agree having extra napkins on hand in case of spills is at least a good idea? And again, why should a waiter harass customers about such a thing? 'I brought you the CORRECT amount of napkins.' Like, you don't know me and my dinner guests, I asked for more napkins, what else are you here for? If I ask for 100 napkins, bring me 100 napkins.
Seriously, how clumsy are you and your dinner guests? As long as you have a napkin each, you're good to go. If you need more napkins in case of a spill or accident, simply ask for more. Otherwise what you're proposing is something that increases the potential for waste, and for unnecessary restaurant overheads.
And no, if you asked for 100 napkins that would be completely ridiculous and I wouldn't be surprised if a restaurant owner or waiter simply told you no, unless of course you had some sort of extreme emergency. A restaurant is selling you food and a good service, not bulk orders of napkins.