The point is that you keep paying the installment every month without having to lift a finger yourself. Regarding special repayments, there are definitely many people who plan with a lot of special repayments but in the end do not make any and end up with an excessively long financing period. A small side note is that special repayments are usually made only at the end of the year, and a few extra interest charges accumulate over the year while the money in the bank still incurs negative interest. It's not the end of the world and won't break a financing, but somehow it's also unnecessary to throw another 200€ to the bank every year...
Especially since you have the option to change the installment multiple times, I would do it directly through the installment. With 2500€ you automatically have about 10,000€ in special repayments. The remaining [Nette] is still great and I wouldn't expect sleepless nights because of that.