"*.35 Whelen is based on .30-03 (or, arguably, .30-01), not .30-06. "
Yeah.... decidedly NOT based on the .30-01.
The .30-01 was a complete and total dead end. It was never manufactured in quantity, it was never manufactured commercially, and it was extinct by the time the .35 Whelen was first designed.
The .30-01's primary characteristic was that the rim was substantially thicker than the rim that was finally adopted in the .30-03 cartridge.
As for whether Whelen based the case on the .30-03 or the .30-06 case... either could be the case, actually.
First, I personally subscribe to the theory that Whelen did NOT design the cartridge, James Howe did and it was named for Whelen. Whelen even said as much in his book "The Hunting Rifle: Design, Selection, Ballistics, Marksmanship."
But, I think it's more likely that Howe DID start with the .30-06 case, not the .30-03, because at the time the cartridge was designed, he was working at Frankford Arsenal (as was Whelen) and would have had TONS of .30-06 brass available to him with which to experiment.
.30-03 brass, on the other hand? Not so much. It had been out of government production for almost 2 decades at that point. Winchester (I believe) was still manufacturing .30-03 brass/cartridges to supply the Winchester Model 95 rifles so chambered (guess what case the .270 Winchester was based on?), but yearly production was tiny and the .30-03 would go extinct in a few years.
Yes, directly necking up .30-06 brass to .35 will shorten the case. But guess what Howe/Whelen had TONS of at hand when the .35 Whelen was being developed?
Arsenal produced formed .30-06 cases that hadn't had the final neck trim done.
Necking an untrimmed .30-06 case up to .35 caliber and then final trimming to 2.494 is a very simple thing.
Anyway, that's my take on it.