@kinggi My personal opinion is that while the products have different variations, they are different products right, and I am guessing they each have their own specific use case. I have seen in the past where its the same product but each sku was just a different count, so like 1 pack, 6 pack, 12 pack, and they all used the same image. They all had different price points though. With that example though, some people want the larger packs right so that is a legitimate product and recommendation that should be made. I am looking more into this but my memory tells me there is nothing out of the box. Here are some quick suggestions.
1. Seeing that they are real products in the catalog/site, are there different image variations or copy variations for each as well? If so and the idea is to put a solid presentation with variating product images then maybe additional product variation images will help.
2. Are the products ids the same with the last 1-2 values being unique? If so are you able to strip the last value. By doing this Target will see it as the same product ID and consider it the same product if you are passing in the meta data via mboxes. If you are uploading csv files then you can manage this yourself and remove the variations you prefer to exclude.
3. Have you thought about removing variations via exclusion rules within Adobe Target? This is similar to option 2 but you are simply removing from the catalog in the Target UI.
Hope this helps!