I'd very much doubt whether that would be valid considering you were still using trains that left your departure station before 09:30.
The restrictions are nothing to do with the WMPTE area but rather as a result of the fare being set by XC who universally restrict their off-peak tickets to after 09:30.
OP wouldn't be using their Northampton-Leeds ticket until Rugby, where departure is after 09:29 and therefore valid - they would be starting late. When starting late, you aren't bound by the time you could have departed your printed origin station - you merely have to look at what the restriction code says.
Thanks for the suggestions, should've mentioned that my tickets have been purchased by work, so splitting tickets or travelling from elsewhere isn't an option.
I presume this is to do with the Network West Midlands peak restrictions being 9:30 rather than 9, as the ticket would also be valid for travel through New Street.
With Rugby-Leeds being valid off-peak for the 9:42 departure, if I bought a Northampton-Rugby single for the 9:16, could I then use the Northampton-Leeds off-peak return for the rest of the journey.
Yes, that would be perfectly valid. However, I would be surprised if any guard on WMT questioned the use of an Off-Peak Return (away from London) after 09:00, as that would be the time they're expecting. Very few seem to have a sufficient eye for detail such that they'd notice it's a 2V (09:30) restricted ticket. You could even ask at the ticket office on the day as to whether you are allowed to travel on the 09:16 and they might say that you are.
The restrictions on any particular ticket have nothing to do with whose 'territory' the journey passes through - it's purely to do with the restrictions that the company that sets the fare has chosen. WMT generally choose a restriction of CS for their Off-Peak Returns away from the London area of their route, and that means that you can use that ticket at or after 09:00. By contrast, CrossCountry generally choose 2V, which means not before 09:30. And yet Virgin Trains often choose 2T for their longer tickets away from London, which means not before 04:15(am)

!
You can find out which two-letter restriction code applies to a particular ticket by entering the origin and destination of your ticket at
www.brfares.com, or alternatively it will be printed on the ticket. You can then look up the meaning of the code at
www.nationalrail.co.uk/XX, where XX is the code.