Just to add, don't be discouraged that you may have gotten a generic email! The fact that you heard back at all is a good sign. Most PIs don't have time to review your application before you apply, most of times it's just because they don't have time.
I've had PIs who emailed me back with emails saying the same things as your email (ie encouraging me to apply) and explicitly telling me that due to the volume of inquiries, they can't answer my research related question at this stage, and if I proceed to later stages of applications they will have more in-depth discussion with me, which was fair. And for one of them I did get to the "later" stage, so getting such a email doesn't necessarily mean that they are not interested in you.
So definitively email, every PI is different and you might be able to connect with some PIs before the application, and if not, at least your name is on their radar. There's a lot of good suggestions above already on what to ask!