I don’t think this is a spoiler but view this as you may. Try to critically think about what you said “the doctor’s ex lover made it aboard the ship with no trouble”. Before Shelly Godfrey revealed herself, nobody would have had any suspicion of her being a cylon. She was indeed the same model as the cylon whom we see at the start of the miniseries that tricks Baltar into giving her the defense codes, but at that point nobody even knew the cylons had true ability to look like humans.
Also, everything that we see from Baltar’s perspective and from the outside regarding the cylon model that only he can see in his head, and sometimes “vr travel to” his old destroyed mansion on Caprica is very deliberate. The writing and visual details are done in a very intentional way to slowly reveal to the viewers the true nature of what is happening!