Let me preface by saying I don't think any of this will be as bad for you, since your trip is later. July and August have already been easier, but not completely easy.
Someone on the Tokyo Disney social media site I frequent said that there was an option to just add nights once you booked your package. I asked about it more, but never got an answer. I didn't see an option to add hotel nights until my hotel only dates were released. It was not easy for me at all. I am also going mid-June and staying at Miracosta. Miracosta and Fantasy Springs Hotel are the only ones that are getting Happy Entry for both parks starting once FS opens. So, demand has been very high. I also have 2 packages that overlap, 3 day/2 night and 2 day/1 night, to get 4 days in the parks. I thought I would cancel the 2nd package after getting hotel rooms for those night, but we decided to keep them. Both packages are at Miracosta, but they were in different room types. That night booking was crazy; I waited 3-4 hours in a queue. I eventually got both packages in the same room type. Supposedly, they will let you stay in the same room; however, it's definitely not guaranteed. I had to book Disneyland Hotel for my hotel only at first, because Miracosta was literally gone in less than 2 minutes after being released every day. I did eventually get Miracosta for those nights after just trying almost everyday/multiple times a day. Still not in the same room type, so I am still looking for the night before our packages start and the last night. Hotel room only is more difficult to get, because they release packages first and release the best rooms with the packages.
I think they expect people to be staying somewhere else, probably locally or actual locals, and to start the package part way through the day. It's weird to me, but I really think they are geared for the Japanese market, not foreign tourists. You can get your package as early as 6:30am from the hotel, drop your luggage, and start your day early. Many people stay nearby at Hilton or Sheraton.
Since I haven't been yet, it's hard to say how much time will be needed. It depends a lot on how crowds are at that time. My impression is that 2 days per park is really needed, but if you don't have the time, you don't have the time. Do what you can, but don't sacrifice Tokyo.