I don't know why that would be a problem, but I'm not a major expert on the linker.
The relevant commit that changed the way the static library is linked is 49b384f. The build flag changes are:
GENERATE_MASTER_OBJECT_FILE = YES;
EXPORTED_SYMBOLS_FILE = Source/CouchbaseLite.exp;
GCC_SYMBOLS_PRIVATE_EXTERN = NO;
PRELINK_FLAGS = "-objc_abi_version 2";
The first one merges all the .o files together into a single object file within the library; it's necessary for making the export changes work. It sounds like that's what's causing your problem, although I don't know why there are still references to .o files or why your build commands end up needing them...
—Jens