He does not establish that the shirt was also bunched up identically.
Common sense experience tells us that jackets & shirts only align in identical positions when in conventional postures.
As you quoted from the article:
In order for the holes to align precisely, one or both garments must have been slightly askew.
So, for the bullet holes to align perfectly, the shirt and jacket did not align perfectly. They were close, but "slightly askew." Thus, no need for the shirt to align precicely with the bunched up jacket. Only the holes have to line up. Thus, your common sense experience test is satisfied.
The author goes on further to say:
I would like to make one point before I address the photographic record, a record that is ripe with photographs and films of John Kennedy's jacket, yet shows precious little of his shirt, and nothing of the back of the shirt which concerns us here. In regard to the photographic record and the shirt back, it is inappropriate to speculate about that which cannot be seen. Yet, the issue must be dealt with in some fashion. Because the holes in the shirt and jacket align with one another, and if the jacket was flush and in the normal position when the shot struck, then the shirt must also have been flush and in the normal position. Conversely, because the holes align, if the jacket was elevated when the shot struck, the shirt must also have been elevated. That logic serves to conjoin the discussion about the photographic record of the shirt and the coat for the purpose of this essay.
I would also add that if the shirt was not bunched in a manner similar to the jacket (but not necessarily exactly---remember, "slightly askew" for the bullet holes to match), then an alternate explanation accounting for one bullet hole in the jacket with no corresponding hole the shirt and a second bullet hole, in the shirt, with no corresponding hole in the jacket, is necessary. Or, alternatively, one could postulate the holes were not bullet holes at all. But then one would have to explain how Kennedy got a bullet wound in the neck/back area without getting any bullet holes in the back of his shirt or jacket. Or, one could postulate that Kennedy wasn't shot in the back/neck area at all.