Sure, but what an AV is going to look for is code that manipulates executable files, not random binary files. If the patchers are designed to apply patch files to ROMs rather than having the patches embedded then it makes even less sense that they get flagged.

> It sounds like this site is packing the two together,

1. No; as you said, no ROM hacking site distributes the original ROM. This one is no exception. They don't want to flagrantly violate copyright. (And in fact, modern patch formats — xDelta, UPS, BPS — are designed to avoid even minor "quotations" of the original copyrighted material, by using "copy offset:length" ops, or by storing partial/sparse patch segments as XOR deltas of the old and new files.)

> and the patchers are causing the flagging issues

2. No ROM hacking site distributes a patcher executable along with the patch. It'd be a huge waste of both bandwidth and storage space on their CDN. Besides the very reason coming up here (novel archives containing executables make anti-virus programs unhappy), there's also the fact that modern emulators, when loading a ROM, will auto-apply a patch in-memory if one is found in the same directory + with the same basename as the ROM. (Similar to how VLC auto-loads subtitle files if found beside a video file.) Creating an on-disk modified ROM using an explicit patcher utility is, for the most part, unnecessary today.

FYI, I downloaded the first ROMhack I saw from the referenced site (romhack.ing). It was a .zip file. Decompressing it, all it contained was a set of .ips files (variants of the patch) and a README.txt.

In short, there is no inherent, structural reason that a site hosting only archive files like this one, would trigger any anti-virus system.