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I fully agree, this is very annyoing - just have a look onto the attached screenshot (I just added a 4 columns (ok) plus their MS_Descriptions and the whole compare becomes an unreadable mess
maybe it would already help, if you change the syntax in your created scripts to
EXEC sys.sp_addextendedproperty @name = N'MS_DESCRIPTION', @level0type = N'SCHEMA', @level0name = N'schema', @level1type = N'TABLE', @level1name = N'table', @level2type = N'COLUMN', @level2name = N'column', @value = '<column description>' ;
(name the parameters and move the @value to the end of the line).
Or use a logic similar to the logic for static data (there you are able to identify new / changed / deleted / equal rows). As primary key you could use the object_name + column_name (maybe not the id (except force column order is enabled), it is more likely that you have the the columns in the wrong order than that you rename columns).