Do you oscillate your diet along with your riding?
Either is fine - in fact on this timescale there's not much difference.
My suggestion:
I suspect that what's most satisfying for your body and your desire to measure will be somewhere between the two - probably something like 2300 Cal on your off days and 2900 on your riding days.  This should be quite achievable - a handful of cheese added to your pasta example and another energy bar on your riding days and you're well on the way.
Reasoning:
The human body is very good at averaging out calories burnt and calories taken in.  This is easily demonstrated: the recovery eating phase lasts several hours (though tapering fast especially regarding glycogen), and carb loading (not needed for up to 90 minute efforts) happens the day before the ride.  You'd see a weight fluctuation if you weighed yourself daily, but that happens anyway and hydration would affect that too.
If you're trying to maintain your weight and muscle mass, with that sort of level of riding, you should be fine with a sensible  balanced diet eaten to hunger - tracking your calorie intake isn't necessary, but if you want to do it, that's fine, except that your estimate of your requirements may not be perfect.
Your body can store enough glycogen for that much effort, so losing muscle mass to fuel your rides really isn't an issue, especially as you're snacking.  If you're worried, some small protein intake during/after the ride would do no harm (even just the little bit you get from energy bars with nuts in, for example).  I sometimes do a 75 minute early morning fasted ride (32km, just under 800  Cal which seems like a good estimate - yours seems high but not implausibly so).  In that case I start a protein drink towards the end, which seems to help my recovery in terms of muscle fatigue/aches.
I take your uneven pattern much further - every couple of weeks I do an all-day or even all-weekend ride, and then you really can't take in what you burn (Strava says 8000 Cal for Saturday's 400km).  The excess hunger lasts 1-3 days, but my weight recovers in a similar timescale (when I first started distance riding there was a permanent drop after each long ride, but as I didn't get weaker in the gym I don't think it came from muscles).  Yes there's some energy-dense junk food in there, but that's optional; I happen to like chocolate.
As for your worry about the stress of fluctuating intake - yes, it's fine.  Most of our human ancestors had no choice (could they afford much more than rice/potatoes/bread every day, with meat once a week - or what could they gather in season, how often did they hunt successfully) and anyway couldn't measure their calorie intake.  Your bowel movements might settle into a new pattern, but I wouldn't expect so much as a mild stomach ache