Very interesting question. I'm okay with this question being here since you specifically ask for the effect of rogue planets on Earth's atmosphere. Thinking "astronomically" could be useful in coming to conclusions about whether or not your idea is even a possibility.
When I saw this I instantly thought of ice cores, since trapped gas bubbles could tell you about the composition of the atmosphere. Unfortunately ice cores go nowhere near that far back to be able to tell you about the composition of the atmosphere during the Mesozoic.
Now for the answer:
I can't really speak to the title of your question effectively, since I am unaware of any research involving rogue planets and atmospheric stripping, however, from an astronomy point of view, here is one other thing I would like to point out that may work to reduce the thickness of the atmosphere with time.
- A small fraction of the gasses of the atmosphere exceed the escape velocity of Earth at any given time. Over time, many of these gasses get bombarded by high energy photons (as well as other particles) and fly out of Earth's gravitational potential well. If there are no other sources of these lighter gasses then there is a net loss.
Temperature does play a key role here (as the above plot suggests), but regardless, this process works to reduce the amount of atoms and molecules in the atmosphere (and it affects smaller mass atoms/molecules more so than heavier ones - this is why the Martian atmosphere is primarily carbon dioxide. Essentially it wasn't massive enough to be able to hold on to its lighter gasses, and over time the vast majority of them escaped).
If you had temperature information going back as far as the Mesozoic era, you could in theory run the clock backwards by running a simulation of the evolution of the atmosphere. I don't know how helpful this would really be (or how accurate), since there are potentially other things like volcanic outgassing and the bi-products of living things to complicate the situation. Quite honestly, I know little about these topics and so I couldn't tell you whether there is a net loss or gain of atmospheric gasses.
- As far as rogue planets are concerned, I would find it rather unlikely that such a massive object would still be lurking around the solar system between about 252 to 66 million years ago. The early solar system was certainly more chaotic than it is now (for example, Giant impact hypothesis: $\sim 4.5$ Gya; the collision which caused Uranus' tilt: a few billion years ago), however it is not out of the realm of possibility.