Analysis of the chord on the fourth beat where the timpani plays shows that virtually the ENTIRE orchestra is playing an E.
Exceptions are:
Trumpet 1 (G#), Trumpet 2 (D), Trumpet 3 (B)
So, the "ink" in this case is a chord tone (D), the least desirable (for timpani) seventh of the E7 chord. But, again from rule #1 (ears) & #3 (common sense) in context the root of the chord (E) sounds much better in this case.
Now, the next step is to look at the suggested change in context, both of the work in question and the composer's total output. With Mahler you have a composer who wrote well for timpani, and who had access to pedal drums that were in use in some parts of Europe at the time. In Vienna, where he was director of the Opera, the Philharmonic (also the Opera orchestra) was using the same Schnellar timpani they use today. These drums have a single master screw to change the pitch, and no pedals. He would expect such a simple change to be easy, in fact he requires a more complex one just a few bars before between 2 after reh.#111 and 3 before reh.# 112 (bars 123 & 129). Here the D and A change to E and B, then to C and then back to D and A in bar 137, the bar before the note in question.
Now for another question, what if he had really wanted what he wrote? In the case of Mahler anyway, there would have no doubt been one of those "N.B." footnotes in the score mentioning that the D was not a mistake. Because in the case of all three of the composers in these examples, they were very much aware of what was going on "back there".