Drop accents in submission forms
Unfortunately, arXiv's internal search is not smart enough to consider search queries with and without diacritic equivalent.

Searching for "Čech complex" on arXiv's paper titles provides 11 results, all with the diacritical on the PDF.

Searching for "Cech complex" (without the diacritical) provides 7 results, all of which do have the diacritical on the PDF.

A similar search for "Cramér Rao" (51 results, almost all with diacritical on PDF) and "Cramer Rao" (48 results, more than half have the diacritical on the PDF) shows a similar trend.

It seems like it is not a problem at all to have a diacritic appear on the PDF but not on the submission form (your options 2 and 3). It also seems like there is a slight majority of people that choose to include the diacritic everywhere (option 1), which is also what I would do if this is a name I have chosen for my newly introduced method. After all, you do not want most people to get this new name wrong.