I'm not sure I understand that Rory.
The Health surcharge needs to be paid before submission of the FLR(M) application form since the payment reference number needs to be included at section 1.11
In terms of actual payment the requirement is to pay half of the required yearly amount for applications that include a part of a year that is less than 6 months.
Likewise, you need to pay for a whole year if you’re application includes part of a year that is more than 6 months.
As you rightly said the correct payment in your case is £500
So although it's paid before application submission it actually covers the whole of the period validity of the leave to remain.
The FLR can be submitted shortly before the 30 month residency requirement , but you should avoid submitting it too early on the basis that you need to run the second FLR for 30 months to be sure of reaching that 60 month ILR residency requirement.
Sorry if I misunderstand your concern.