For Atalanta it does because Europa League matches were played in MAPEI Stadium (Sassuolo) and Champions League games at San Siro. Because their stadium doens't meet the FIFA requirements.
I think Atalanta's transferpolicy is good. They are holding on their star players like Ilicic, Gomez and Zapata. They are selling younger less expierenced players for a lot of money and they aren't afraid to invest it in more expensive players, see: Zapata, Muriel, De Roon.
It might not be worth it for them. The extra investments and risk associated with it might not be worth the the extra money they'd make by being 5th or 6th instead of mid table. They probably don't make any sizeable gains to their fanbase or commercially by doing the kind of investment that would give them a serious chance at being a top 4 team consistently.
They are at an eternal disadvantage compared to Milan or inter who will see huge gains as soon as they have a good season beyond just the extra league money.
It might make more business sense to them to stay at this size, make good money from transfer market sales and treat any Europa league or champions league money as a bonus. This might be better than investing heavily and becoming dependent on champions league money.
Their fanbase is also much less demanding than inter or milans.
I am speculating ofcourse. Football is a kind of business where there is a lot of uncertainty on whether you get a good return on your investment if at all. Especially if you are betting on the team outperforming other clubs with much bigger brands who'd make much more money if they reach top 4
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Napol’s time as a top 4 contender is over, not just this season but in seasons to come too. Having said that, there is plenty of individual brilliance in that team so it should make for good poaching by other clubs. Can we please sign Meret already to start things off?
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Napoli and to a greater extent Milan have a huge brand. They can make a come back much easier than it is for a non brand club. Their fanbase would get reactivated as soon as they start competing again