I might take the unpopular side to this argument but I personally love the crate and use it quite a bit during puppy hood.
This does not mean I get to take a mental vacation and leave my pup sitting in the crate all day because I don't want to deal with him. The reality is that pups need CONSTANT supervision...this is not something anyone can devote 24/7. Rather than set him up for failure and run the risk of accidents in the house, chewing inappropriate items or developing bad habits I use the crate as a tool.
I see nothing wrong with placing a pup in a crate with a stuffed Kong while one accomplishes tasks that interfere with constant supervision. Not only is it giving the owner a chance to get things done it is teaching the pup what it is supposed to be chewing on. It is apparent the OP isn't using the crate as a "nanny" but as a training tool.
Of course the bonding time, exercise and training are absolutely crucial but it sounds like the OP is doing this.
Dogs energy levels peak early in the morning and in the evening. They usually spend the rest of the day napping. It sounds like his evening peak is between 8-10PM so I would definitely schedule a play time in there.
As far as rules go...welcome to Doberman ownership. Dobes require a lot of structure and consistency. As long as the rules are set from the beginning and you remain consistent with those rules he will will get the idea. The key is consistency...this means if you have a no dogs on furniture rule it always applies--even on the days you are home sick and want a snuggle buddy. My experience with Dobes is they like to test your boundaries to see just when and how much they can get away with. If you are consistent, after a few attempts they leave it alone and find another rule to test you on. If you are inconsistent then its the equivalent of "well since my owner cant make up her mind, I'll do it for her: dogs on furniture!"
A short but excellent read that I think all Dobe owners should read is "How to be leader of the pack and have your dog love you for it" which is like $3 on Amazon. It illustrates the everyday behaviors we do that convey leadership to our dogs. This info is priceless when dealing with a bossy pup.
I do agree with the part about him having too much freedom. Along with the NILIF lines, he only gets as much freedom as he has earned. Try using an Xpen and blocking him off in the room with you.
Tying him to you is an excellent idea that was brought up.
Congratulations on your little guy!