You are correct, the agile trait reduces the MAP penalty on its own attack and isn’t dependent on the previous attack being agile.

In general, for a small damage dice size difference, I believe agile is about equal. Consider that for an average 1 damage difference between a d6 and d8, agile will miss 5% less and crit 5% more at MAP-4 than a d8 at MAP-5, making it wholly worth it. This difference becomes even greater at MAP-10 vs MAP-8. However , a dice size increase is worth roughly two traits (you can see this by comparing average quantity of traits across damage dice size) which means agile is one trait worth two during MAP as it averages out to equal with a weapon of a bigger size.

This means that a d4 weapon with 4 traits where one of them is agile has a ‘trait’ economy of 5 traits during MAP as it averages a d6 weapon’s damage but still retains the other traits it only gets due to being d4.

I don’t have raw numbers for an extreme example I.e. d12 and a d4 agile but the rule of thumb is it pans out super slightly ahead on average in small dice size differences iirc