You can decline tyres and fuel and just drive through to fulfil the mandatory pit stop requirement. With base fuel and tyre wear, I reckon they've added it solely to try mix things up, especially with people bringing their own tuning setups. Say you find you're being held up early in the race by a train you can't find an opportunity to move through, you've got the option to try taking your pit stop early to escape to free air and attempt an undercut.
I can't say anything for the second question though, maybe someone here has more experience tuning and can give you some tips. I've simply come at this as picking a manufacturer I fancy playing and then trying to make the best tune I can that gets under the limit (without doing all the transmission exploits, I simply refuse to take part in that even if it means it will be a miracle to win). I've had to mess around with the Aston Martin just to get it under the 630PP limit since it starts off higher than that.
