Several of the SMW hacks shared have been 4-byte alterations of roms I've already datted (I can't say for the other games). With few exceptions, I simply dat what the patch outputs, nothing further, to preserve the result as what the producer presumably intended. If the result rom's checksum mismatched the header, 9/10 times it's because the author's source rom did also, due to post-save label edits or further modification by tools which don't care to maintain this unaffecting data.
Are you fixing the header checksums for a purpose? AFAIK, "cleaning" roms by modifying the internal checksum is only being disingenuous about the true nature of the data. When a car is trying to report a problem by flashing a check engine light, you shouldn't reset its status codes and call it okay. Imagine if No-Intro does this to "fix" dumps of actual cartridges that actually had bad memory cells. This is now one of the areas I'm considering be filtered out to reduce duplicates, so unless there's a compelling reason, I'd like to not have to keep adding them as (CRC Fix). So far only 10-12 of them from you, but I know of at least 2550 candidates for this type of alteration.