There are more children applying for relatively fewer selective places. Croydon has added around 80 additional primary classes in the last decade, so there are 2,000 more pupils in just that one borough. And whilst the number of state school places has increased, even in the grammars, the independents haven't increased their places to the same extent, if at all. A similar issue arises in all of the boroughs nearby, and given that schools such as City, Dulwich, KCS, SPS etc have kept their numbers steady, competition for the independents has risen.
"does this mean that an applicant at the lower end of the new grammar entry point (i.e. with 90+ more places) is not necessarily someone towards the higher end of the indie entry point that would merit a scholarship award?"
Yes, that certainly seems to have been the trend over the last couple of years. I know of many boys who did get Wilsons, but no scholarship. Bear in mind that there are some very bright boys from well-off families who wouldn't necessarily consider the grammar schools at all, especially in a period of austerity, so there will be boys at the top end of the indie scale who aren't in the grammar pool at all.
Equally Whitgift in particular will acknowledge that Maths and English aren't the only measure of talent, and they do need to find at least 100 full fee payers in each yeargroup, so the overall range of ability is wider. Due to the fact that it has fewer places, and is also cheaper, the range isn't quite as wide at T. Whether changes of head will make a difference, time will tell I guess.