This is correct as it is rather complicated for the engine to be set to check that there are no Axis units interdicting the route from Murmansk to... well where is a good question.
For instance, if the checks were stopped too early e.g. at Belomorsk, then it doesn't really resolve the issue as the Axis could have taken everywhere south and east of Belomorsk, but if places further south and east are checked then it gets more tricky as there is more than one route from there, while equally importantly, there would need to be no Axis units along the route.
Essentially it would require a string of dummy scripts nearly as long as the Great Wall of China to implement, and one could also argue that supplies delivered at Murmansk could in the warmer months be shipped by the Soviets to Arkhangelsk.
Bill - I have no idea how the engine scripts work, but could you not program it to check in just two places - Belomorsk and Vologda?
If the Soviets can trace an unbroken rail line north from Belomorsk to Murmansk, then that convoy route is open; and if the Axis cuts the rail line anywhere north of Belomorsk, then the convoy shifts to Arkangelsk (regardless of the season). If the Axis cuts the rail line south of Belomorsk and Belomorsk is still in Soviet hands, the Soviets can shift the resources from the Murmansk convoy further east along the rail line that runs from Belomorsk to Vologda, so the Murmansk convoy is unaffected. However, if the Axis cuts the rail line at Vologda, then both convoy routes are cut and the convoy ceases to function. Ideally, you would have to scripts also check to see if there was an open rail line south from Vologda to whatever city is the current Soviet capital - but if that requires a "Great Wall of China" of dummy scripts, then just checking for control of Vologda itself is a pretty good proxy for success by the Axis. It seems to me there should be some overall effects on the Allied convoy of cutting those rail lines and it provides an additional strategic incentive for the Axis to push into northern Russia once they have captured Moscow.
Adding checks for who owns a resource is pretty easy and I have thought of adding more locations, and perhaps having the ownership of every resource checked between Murmansk and Belomorsk, plus Vologda is the best, as all would be required for that convoy route to work.
Now, this would just be checks for ownership of the resources, so if Axis units have crossed the railway line but not taken any of these resources then the convoy would still provide the USSR with MPPs (adding checks for this would create the mountain of scripts that I mentioned) but the situation would then be a lot more reasonable and realistic than at present.