These cars were not made like today's: they required a lot of fitting and tweaking as they were assembled. My TD did much the same thing as yours, but worse. I had trouble making the hook on hood latches line up with the square hole in the mating piece. I solved it just by loosening bolts, moving things around as much as possible, and similar fiddling. At the time, I wasn't aware of the cowl-rubber issues. I do agree that it's not expected to be a tight fit, but it still must fit well enough for the latches to work.