It's more complicated because the Irish law people were following was found to be invalid, not that the people leveraging it we're breaking the law as understood at the time, but it still seems unfair to call this approach legitimate.
It wasn’t found to be invalid per se. The European Court of Justice found that the tax breaks Ireland was offering were unlawful state aid (a corporate subsidy that violates EU law) in the case of large multinationals such as Apple. From what I understand of the ruling, it only applies to large multinationals, and Ireland is allowed to continue to offer the same tax breaks to smaller firms.
https://curia.europa.eu/jcms/upload/docs/application/pdf/202...
Also, while IANAL, I have read some EU law textbooks, and one thing they make clear is that ECJ decisions do not always have “direct effect” - the ECJ can declare a national law to be in violation of EU law, but whether that by itself invalidates the national law depends on the specific grounds the ECJ used. So, without having looked into the legal details of this specific ruling, I’m not even sure if it makes the Irish law invalid, as opposed to merely illegal. The distinction is, an illegal law, the national government is obliged to repeal/amend it, and if they fail the EU can punish them, but it remains in force until they repeal/amend it; whereas an invalid law they have to immediately stop enforcing it.
Ireland, since the mid-1980s, has been offering Apple (and ONLY Apple) a bespoke tax arrangement which is not only unlawful state aid under EU rules but also straight-up illegal under Irish law as well. This "deal" was never codified in primary or secondary legislation in Ireland. The government of famously-not-crooked-in-any-way Charlie Haughey did this deal under the table, and all subsequent administrations have been behaving like it was legal. It never was.
Apple was treated differently to all other companies -- those companies were subject to the laws at the time which allowed multijurisdictional shenanigans as described in the OP link. There was never any legal basis for Revenue's different level of enforcement for Apple alone.
Those activities were not illegal at the time. If the laws have changed, then as a tax paying entity, these people/businesses will have to comply with the new laws and/or remove themselves from the jurisdiction where these laws preside.