Compliments on your detailed and useful topic.
"The 1884 onwards register has been edited, due to the large number of registered items. ....."
Mostly bottles seem to be missing. This deficient Thompson list goes up to February 28 1908. After that date the blue book takes over, and I think it is complete, but I'm not aware of anyone doing a thorough check in recent times. The others you mention sourced from Thompson or from Thompson's source, the MS list at Broadfield House. Also these lists are Class III Glass only, and, as we have found here on the GMB, glass items were sometimes registered under a different class, most frequently Class IV Earthenware. Two of the possible explanations are that it broadened the protection to pottery and china, and that it significantly reduced publicity, particularly to US glassworks, who would have regarded any Class III registration (or glass patent) appearing in PG as an OK to make it themselves.
Editing primary source material should be discouraged in the strongest terms. Also praise should always be given to those who publish completely and without any editing, like Eric Reynolds (Walsh factory pattern books) and Pamela (trade catalogues).
See Marsh, M., Perfume Bottles — A Collector's Guide, Miller's, 1999, p.28. This also shows a near spherical Crown bottle, not shown in your link. My pencilled marginal note reads "1st Series Reg No 260854 — 2/3/1872". Nice to know I got it right.
There is at least one 1884 registration which has the Rd number inside the old lozenge, and it has been mentioned here on the GMB. It conjures up a lovely picture of a mouldmaker being given the newfangled Rd No without any details of what to do with it — and then doing his best to cover any eventuality. Wouldn't that be a wonderful subject for a collection — Registration mark errors and oddities.
Finally I have had your first bottle through my hands without any base marks at all, probably a late example.