The question appears to be: can Gecko's merging do what Wrye Bash does with its magical bashed patch? So far, it seems Gecko cannot, or am I mistaken?
You have to keep two things in mind:
1. Bash takes all loaded mods into account, Gecko only the ones you've selected.
2. Bash has import functions to handle specific differently. Gecko does not, is therefore a lot more "blunt" in combining.
Which can be a good thing, and which can be a bad thing. Example given let's say you've got one mod giving NPCs new eyes and hairs (let's call it NpcDiversity), another one giving them new face structures (let's call it TNR). Both edit the same Import category, therefore cannot be merged in Bash's bashed patch (last loaded wins). In Gecko though they are combined, because Gecko looks for each subcategory individually. But if you look at many mods editing leveled lists, which need to be combined in a quite elaborate way (let's call it FCOM), using Gecko's merging will result in mod soup. Or let's say you're running LAME, after that Supreme Magicka, and after that LAME's shaders. LAME's shaders are an import graphic mod, therefore doesn't overwrite SM when using Bash. Gecko although will take the whole magic effect settings, not only the visual ones, therefore would reinstitute LAME's settings.
Both Bash and Gecko are different tools, with different purposes. As a modder I can say I need both. Players most likely will only need Bash - Gecko is much more a modder's tool than a player's tool.
One of the three "big no"s of merging is to not merge mods that have files depending on them. All magic overhauls have. If you want to use any file depending on them, you'd have to merge all of them together. Which can be quite a task, and the more files there are, the more likely mod soup becomes.