It’s going to be better to have the interest paid into your ISA as this will increase your amount of tax exempt cash that you have available to invest.
But if you don’t want this, you can always ask customer services to move the cash from your ISA to your GIA. But the only reason I could think of doing that is that you want to invest in shares that cannot be held in an ISA?
Freetrade just give preference to interest earned to your ISA - so the interest is paid into the account on which it was earned.