The max fines are based on the top-level parent company's global revenue. Instapaper was owned by Pinterest until being spun off very recently.
Most likely, Pinterest's lawyers and executives were not OK with risking the fines, and also did not want to devote enough development resources to GDPR compliance for such a small subsidiary like Instapaper. Also explains why they'd spin it out -- GDPR changed the calculus.
This is speculation, but I've seen this GDPR fear play out elsewhere. Large parent companies are very worried about those worst-case fines and want to ensure there's no risk whatsoever.
The "Instapaper must be up to something sketchy if GDPR compliance took so long" narrative here seems pretty unfair. If their former owners are to blame for the long EU outage, it's understandable that Instapaper isn't going to publicly call them out -- they may even have agreements preventing this. And the whole spin-out probably took some time and logistical effort, so they couldn't reasonably focus on GDPR immediately after that either.
(Edit: not trying to knock Pinterest either; their actions would be completely understandable given the max potential fines.)