If you intend to only take 3.1% on the original 100 EUR, that's not what this formula is going to calculate. That formula is assumes that you're taking 3.1% of the entire charge, including the bit that you're adding to account for the fixed & variable Stripe fees.
If that's the case, your target amount should be 103.1, so the formula would be:
total = (target - fixed) / (1 - percent) = ((100 * 1.031) + 0.3075) / (1 - 0.01722) = 105.2193
If you submit a charge with that total, the amount left over after the Stripe fees is 105.22 * (1 - 0.01722) - 0.3075 ~= 103.10. From the connected account's perspective, your application fee is also deducted, leaving them with exactly 100.00.
I'm a bit confused, though, since this formula will yield fairly different results that the one you're using - ie: off by tens of cents, not fractions of a cent that will often be rounded away. I may have misunderstood how you're setting this up. To confirm, my understanding of what you're doing is that you're creating a charge with amount=10539, application_fee=310 - is that correct?