The daughters he did have married into Scotland and France, but Arthur and Margaret are close enough in age that a female counterpart to Arthur (Edith, after Henry VII maternal great grandmother) would probably have matched up with James IV.
Let's say that Edith is also luckier than Arthur, doesn't die within a few months of the wedding, has several children and lives the equivalent life span to Margaret and dies further down the line.
Elizabeth of York likely lives longer as she isn't pressed into producing another spare, given Henry VII and Elizabeth have long since cone to terms with a daughter being monarch after.
Henry VII died in 1509, but Margaret Beaufort lived to age 68, so a healthier and not heartbroken Henry lives to 1524 and then dies. Edith becomes Queen suo jure, with her second husband as King jure uxoris.
Edith dies 1538, by which point her son James V only serves as King for four years before he dies, amd the heir of both Scotland and England is OTL Mary, Queen of Scots, only a handful of weeks old. A Regency occurs in Scotland, but England changes at the idea of not only a Scottish ruler, but a Scottish regent to a child Queen.
ITTL version of Margaret Douglas is offered the crown of England. But does she accept?