I agree with your sentiments.
Your question about how I would feel if I owned one with the disc printing and then one came out on the crystal.... would I be mad? Absolutely. But in the case of the owners of the 25 piece LE of course this is not the case - they have what I view to be the "correct" printing. And for brand Purists like yourself, I speculate their 25 piece edition will be the one held in highest regard. Would I choose it over the 62 piece charcoal PVD edition? No, but surely they bought what was the original concept for the watch.
Let me tell you about a RG Aero Bang I owned (and I know you are not a Big Bang fan, but hear the whole story first). I acquired one of the first pieces delivered in the US. When I opened it I immediately noticed the bezel was polished (instead of brushed, as the "production" pieces were supposed to be) and the crystal was completely clear (whereas all other Aero Bangs have the Hublot logo printed on the underside). I was not sure I preferred the bezel, but I LOVED that there was no logo on the dial or crystal. I thought it was very unique to be unmarked aside from the straps and clasp and caseback. Clearly any watch person would recognize it as a Hublot Big Bang. I ended up selling it, for various reasons.
But I ask, what if JLC abandoned all logos on this watch's dial and crystal? Is it written somewhere a watch must have the brand name attached? Surely a Royal Oak needs no AP to be recognized, a Luminor need not say Panerai. Of course this NSA is not an "iconic" watch by any means. So maybe JLC needs their name attached to it. But I will tell you honestly, if the change was made to abandon the logo altogether instead of putting it on the disc, I still would have acquired one from the 1500 piece LE.
Now I have this micro edition with the printing I prefer, also adding some unique touches. Overlooked so far but something I am excited to see is the "two tone" look of the charcoal titanium's dial. Black outer dial with numerals and date, charcoal center and case. Sounds awesome.
I guess this one is easy for me, because my major brand allegiance is to Audemars Piguet. We have discussions like this too. As JLC is just beginning to grab me, I don't yet have the attachments and deep opinions I surely understand others do. It's quite nice actually, I can simply select a watch that looks great to me and have no other concerns!!
Be well my friend, and stay warm. If it makes you feel better, the last 2 days here were single digit temps, and below freezing at night. Brrrrrrrr........