As the Scottish government says:
The headline estimates of Scottish public sector expenditure and revenue in GERS embrace two key principles:
1. Public sector revenue is estimated for taxes where a financial burden is imposed on residents and enterprises in Scotland
2. Public sector expenditure is estimated on the basis of spending incurred for the benefit of residents and enterprises in Scotland
I added the italic, bold emphasis.
GERS compares tax paid in Scotland with spend for Scotland. That earns the following are ignored:
Scottish income taxed outside Scotland e,g. rents, interest, profits, royalties and maybe more, all of which can be significant;
Well, yes. Suppose it does. And as an independent country Scotland won’t be able to tax those incomes accruing to people outside Scotland. So it seems a perfectly reasonable basis upon which to base the economics of an independent Scotland, no?