Interesting situation!
1. I would insist on the quiet time every day I think it's crucial that they get the down time in their cot to recharge, I think the day is just too long without a little rest. My son will play happily in the cot paying quietly for an hour, he only naps half the time. He comes out much more recharged. Look at it like you are doing them a favour, teaching them how to switch off and have down time, everyone needs to learn that!
2. If they won;t go to bed without eachother and you must do their routine together, then I would do everything as normal and bring the routine forward to suit when DD needs to go to bed. I think it's fine if DS is laying around for a while, its all rest. MY DS will sometimes lay around for up to an hour before going to sleep. He doesn;t mind, he lOVES it in his cot, its his safe litlte place to play with his stuffed toys. I would try it and see if your son will comply. If he doesn't and disturbs her sleep then maybe you'll need to try staggering them into bed. I would do everything the same up until bedtime, then put DD down and read DS one more story. Maybe you could talk about it with them during the day preparing them, saying that DD is very tired and needs to go into the cot first today. ANd make it special for DD< saying she gets a special teddy or something for going first, and then DS will come later and give her a big kiss in her sleep.... what ever makes them both feel special about the change. I would try not to compromise DD's bedtime too much, as she will only become OT and cranky after a few days of not getting to sleep early enough, and then your life will get really tough. The OT builds up over time, and creeps up. We were find for a few weeks, then he became a mess.