It occurred to me that a better solution would be to constrain the "if*" commands matched by the regexp produced by LaTeX-indent-commands-regexp-make. My earlier patch fixed the preamble definition, which was all that mattered for the specific tex file that I was editing, but it is more natural to simultaneously fix any uses of such commands. I've attached a patch which gives my best attempt at doing this (no claim of optimality).
0001-fix-indentation-issue-involving-user-defined-if-comm.patch
Description: Binary data
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