Here is my solution based on Mike's answer!
My document packages are bundles, with the usual hierarchical structure… So there are four directories that I mutate during saves:
- The save creates a new top-level (My.bundle)
- The Contents directory is changed (My.bundle/Contents)
- The Resources directory is changed (My.bundle/Contents/Resources)
- The localized resources are updated (My.bundle/Contents/Resources/en.lproj)
The recipe starts with adding a mutable dictionary slot to your document class to preserve the contents of each of these directories.
@interface LMDocument : NSDocument {
@private
    // All this is for preserving SCM artifacts across saves…
    NSMutableDictionary * bundleWrappers;
    NSMutableDictionary * contentsWrappers;
    NSMutableDictionary * resourcesWrappers;
    NSMutableDictionary * localizedWrappers;
}
When creating a new document, these start out as empty dictionaries.
- (id)init;
{
    if ((self = [super init]) != nil) {
        bundleWrappers = [[NSMutableDictionary alloc] initWithCapacity:0];
        contentsWrappers = [[NSMutableDictionary alloc] initWithCapacity:0];
        resourcesWrappers = [[NSMutableDictionary alloc] initWithCapacity:0];
        localizedWrappers = [[NSMutableDictionary alloc] initWithCapacity:0];
    }
    return self;
}
When reading in an existing document, replace these with mutable copies of the relevant fileWrapper contents.
- (BOOL)readFromFileWrapper:(NSFileWrapper *)fileWrapper
                     ofType:(NSString *)typeName
                      error:(NSError **)outError;
{
    NSAutoreleasePool * pool = [[NSAutoreleasePool alloc] init];
    bundleWrappers = [[fileWrapper fileWrappers] mutableCopy];
    contentsWrappers = [[[bundleWrappers objectForKey:@"Contents"] fileWrappers] mutableCopy];
    resourcesWrappers = [[[contentsWrappers objectForKey:@"Resources"] fileWrappers] mutableCopy];
    localizedWrappers = [[[resourcesWrappers objectForKey:@"en.lproj"] fileWrappers] mutableCopy];
    NSFileWrapper * infoPlistWrapper = [contentsWrappers objectForKey:@"Info.plist"];
    [contentsWrappers removeObjectForKey:@"Info.plist"]; // Replaced during save…
    // …
    NSMutableDictionary * localizedWrappersCopy = [localizedWrappers mutableCopy];
    [localizedWrappers enumerateKeysAndObjectsUsingBlock:^(id key,
                                                           id obj,
                                                           BOOL * stop)
     {
         if (mumble) { // If it's a file that will be replaced during save…
             [localizedWrappersCopy removeObjectForKey:key]; // Replaced during save…
             // …
         }
     }];
    localizedWrappers = localizedWrappersCopy;
    [pool drain];
    return YES;
}
And finally, when saving a document use the dictionaries so painstakingly prepared.
- (NSFileWrapper *)fileWrapperOfType:(NSString *)typeName
                               error:(NSError **)outError;
{
    NSAutoreleasePool * pool = [[NSAutoreleasePool alloc] init];
    NSFileWrapper * localizedWrapper =
    [[NSFileWrapper alloc] initDirectoryWithFileWrappers:localizedWrappers];
    [resourcesWrappers setObject:localizedWrapper
                          forKey:@"en.lproj"];
    NSFileWrapper * resourcesWrapper =
    [[NSFileWrapper alloc] initDirectoryWithFileWrappers:resourcesWrappers];
    [contentsWrappers setObject:resourcesWrapper
                         forKey:@"Resources"];
    NSFileWrapper * contentsWrapper =
    [[NSFileWrapper alloc] initDirectoryWithFileWrappers:contentsWrappers];
    // …
    for (id item in mumble) {
        NSString * filename = [item filename];
        NSData * data = [item data];
        [localizedWrapper addRegularFileWithContents:data
                                   preferredFilename:filename];
    }
    [contentsWrapper addRegularFileWithContents:[self infoPlistData]
                              preferredFilename:@"Info.plist"];
    [pool drain];
    [bundleWrappers setObject:contentsWrapper
                       forKey:@"Contents"];
    NSFileWrapper * bundleWrapper =
    [[[NSFileWrapper alloc] initDirectoryWithFileWrappers:bundleWrappers] autorelease];
    return bundleWrapper;
}
Now when a package document is edited, the application preserves any files it didn't add to the bundle, including SCM artifacts and "other" localizations!