Again, one more time, the issue isn't necessarily about offending Jewish people. That's not the reason (or at least the only reason) for doing this. They are correcting something that never should have been done in the first place. Like has been mentioned, why don't we use the term Tabernacle instead of Phylactery?
Probably because publishers, knowing that some people, notably many in the US which is their primary market, keep giving value to religions and so they chose to tactically not reduce their potential customer base? Or that many of their potential customers, would subscribe to the idea that "freedom of religion" equals or implies a "need to consider all religions as good things that are deserving respect" and might choose not to buy their products as a result.
This idea isn't necessarily common anywhere, notably outside of the US where there is a very specific view on religions. Elsewhere, freedom of thought, for example, does mean that Flat Earther are free to think the Earth is flat, and might even be able to express it, but it doesn't mean that their belief should be respected: it's not morally wrong, from this point of view, to say "look, Flat-Earthism is a silly idea, let's laugh about it". Same with religions. People have the right to worship anything, but they shouldn't expect others to respect the god their worship or in this case, an item they use in their worshipping practice. This moral position, representative of the culture of atheistic countries, is certainly not common in the US, and Paizo didn't want to lose customers by calling the BBEG of a campaign Saint Luke, because they could lose a few customers that would be miffed by the name choice and a few other, maybe more, that wouldn't care particularly about Saint Luke but would say "hey, they are not respectful to a religious figure, it's wrong of them."
From your post, I dedude that you are adhering to the idea that all religions are worthy of respect by themselves ; which is fine, but it might make you not understand the position of others in this thread, for which religions are not more nor less praise-worthy than Flat Earthism. There are even stronger opinions that all religions are intrinsicly evil, mostly from actively atheistic/anticlerical cultures. I doubt it would be possible to reconcile all these philosophical views to formulate a consensual opinion on the moral use of phylactery.
On the other hand, the argument that "phylactery" isn't an accurate word to represent a soul-storing item isn't based on adhering to a particular moral view on religions, it's... a definition. If the lich was using it as a protective amulet containing arcane texts to protect against death and keep living, it would be spot on to call that a phylactery (albeit morally wrong for some, right for others, depending their philosophical stance on religions), but Paizo chose to make their liches need a soul storing item, and there is no reason to call that a phylactery, because it's not what a phylactery is. It's as wrong to call it a phylactery than to call that a teapot, and nobody would defend teapot. This is, I hope, consensual because it's factual and this explanation isn't narrowed by the need to subscribe first to any moral idea regarding religions.