Software is not a violation of the GDPR. GDPR means you can not use it for some things, but given the focus on a personal storage system it's less relevant.
Yes software itself is safe. But eventually you'll want this stored online. At that point, the company hosting your data will be obligated to comply, but by design, cannot. In that sense, it's worse than simply incompliant. It's virally incompliant. Any software that uses it will also be affected.
The GDPR is effectively irrelevant here unless your goal is to host Perkeep as a service. Yes, if you upload your own personal database to Dropbox then Dropbox does still have GDPR obligations to you but those obligations do not extend to managing your files for you also, as an analogy if you were to upload a zip file to Dropbox it would not be reasonable to expect them to remove a file from within that zip file at your request.
So, you're suggesting this software would prevent a hosting provider from deleting your account data because you've used it for Perkeep data? I can't begin to comprehend the thought process that leads you there.