I am by no means a sports historian, but being an avid football fan, I thought I might take a shot at this.

The 1966 World Cup, the first World Cup held in England, did indeed have significant emphasis on the “Britishness” of the tournament. However, this was not at the expense of “Englishness” - both were very much interchangeable in 1966. The official marketing of the World Cup saw extensive use of the Union Jack. The official insignia of 1966 produced by the (English) Football Association had the Union Jack flag as its background. Football-related publications, such as the official Football Association World Cup Report of 1966, represented England with the British flag. The official mascot, World Cup Willie, had an Union Jack kit on, but was also a lion. The lion was long associated with the English crown stretching back to King Richard I, “the Lion Heart,” along with perceived English national values of bravery, courage and tenacity (Nobby Stiles, the starting holding midfielder of England, was described as ‘the little Lionheart’ both for his stature and his tenacious nature on the football pitch). World Cup Willie was therefore a mix between British and English characteristics, and indicative of the interchangeability of national identity during 1966. The English press also saw Britain and England as interchangeable. The England team was often written as the representative of the United Kingdom, as neither Scotland, Wales nor Northern Ireland qualified for the tournament.

The association between the English national football team and the Union Jack, and by extension “Britishness”, continued into the 1980s. Before 1990, the Union flag or the Three Lions were the sole representatives of the English national team in advertisements. See the blue, red and white trim on the 1982 England football home kit (on a young Kevin Keegan!), and the lyrics of the official English squad song ‘This Time (We’ll Get It Right)’ (a pretty indicative title of the failures of the national squad since 1966) for the 1982 World Cup in Spain:

We're on our way

We are Ron’s (referring to England manager Ron Greenwood) twenty-two

Hear the roar

Of the red, white and blue

However, there was also a growing trend from 1970 onward that correlated the English football team with an exclusively English identity. In the 1980s, there was sporadic use of the St George’s Cross among fans, although the Union Jack remained the preferred choice for the majority. The 1990 World Cup in Italy seems to have constituted a shift in flag usage. In tabloids and lower-end newspapers such as the Sun, the St George’s Cross was used to represent England in match reports, while Coral bookmakers and advertisements in the United Kingdom did the same. The national team no longer wore the colours of red, white and blue, instead moving on to the red and white of St George’s Cross.

The replacement of ‘Britishness’ with ‘Englishness’ was most prominent at the 1996 Euros, which was held in England. The mascot, Goaliath the Lion, wore a completely white football strip. The (absolutely iconic) anthem for the national team, “Three Lions (Football’s Coming Home)”, made no reference to either St George’s Cross or the Union Flag, but the Three Lions, a symbol of the English crown since the 12th century, featured prominently. In all of England's Euro 1996 matches, the St. George Cross was a common fixture in the background. The use of St. George's Cross was not deliberately promoted by the Football Association, and largely seems to be driven by the fans themselves. In searching for reasons for this change, Polley points out that by the 1990s, the St. George Cross had lost much of its far-right connotations that had plagued its use in the 1970s and 1980s. It could be more openly displayed at big international tournaments, although scholars have questioned the direct linkage between flag-waving and a resurgent English patriotism. Furthermore, the Union Jack would make little sense in the 1996 Euros, as England and Scotland faced off against each other in the group stages. From then on, the St George’s Cross seems to have completely replaced the Union Jack among England national team fans.

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Sources:

Polley, Martin. “Sport and national identity in contemporary England.” in Sport and National Identity in the Post-War World, edited by Dilwyn Porter and Adrian Smith, 10-30. London: Taylor and Francis, 2004.

McGuinness, Mike. “Some Reflections on Representations of the England Football Team through Ephemera from the 1966 World Cup to the Present.” 2011. https://idrottsforum.org/wp-content/uploads/2019/06/mcguinness110330.pdf

Abell, Jackie, Susan Condor, Robert D. Lowe, Stephen Gibson, and Clifford Stevenson. "Who ate all the pride? Patriotic sentiment and English national football support." Nations and nationalism 13, no. 1 (2007): 97-116.

Marks, Darren. "Team GB: united or untied? Contemporary nationalism, national identity and British Olympic football teams at London 2012." PhD diss., Loughborough University, 2010.

Gibbons, Tom. “Contrasting Representations of Englishness During FIFA World Cup Finals.” Sport in History 30:3 (2010): 422-446.

Crolley, Liz, and David Hand. Football, Europe and the press. Routledge, 2013.