I've now got my replacement XL Ent-A, previously they sent me a replacement straight away but this time they wouldn't send a replacement until they received the original back first. Not sure if that is general change in policy or just applies to larger value items.
Taking a closer look (no point nit picking over minor details originally when first one had obvious paint damage) apart from the big blue windows on the bottom of the secondary hull there are no indents on the model to indicate where the windows should be. So there are no mis-aligned windows as such. The red circles around the docking ports aren't quite aligned correctly though as there is indent for where they should be.
For me the original Enterprise refit model was the worst in the collection, in fact if it had been the first model instead of the second I likely would never have bothered collecting any of them. I love the Enterprise refit design, it's possibly my favourite design of all the different Enterprise versions. This XL version finally delivers what I had been hoping for. The most baffling thing though which what is generally a very good model is that it is missing the stripes around the edge of the saucer section when this existed on the original regular models. This same issue appears to also occur on the Ent-B from the preview pictures.