The two long-term statuses look near-identical on their requirement lists, which leads applicants to think a choice has to be made between them. The meaningful differences sit in the absence rules and in what each status is worth outside the Netherlands.
Both the Dutch national permit (verblijfsvergunning voor onbepaalde tijd) and EU long-term resident status (based on EU Directive 2003/109/EC) need the same headline five consecutive years of valid residence, an income requirement, and a passed A2 civic integration exam or exemption — the conditions on IND's own pages are essentially identical. Where they diverge is the absence rules: the national permit uses IND's general main-residency test (roughly, no single absence over six months in a calendar year, or four months in each of three consecutive years), while EU long-term residency has its own explicit cap — no single absence over six consecutive months, and no more than ten months total absence across the whole five-year period (Blue Card holders get a more generous twelve consecutive/eighteen total months and can combine residence time across EU countries). You don't choose between them: the same application form covers both, and IND assesses your eligibility for the EU version alongside the national one and grants whichever you qualify for. The practical payoff of the EU version is portability — an eased, though not automatic, path to residing and working in another EU member state, where the purely national Dutch permit means nothing outside the Netherlands. Fees are the same for both, so there's little downside to applying for whichever IND says you qualify for.