I agree with everything that Travis said… the reason why you are witnessing different number of total links is because of the index you are using! GWT will give you limited amount of data where as Open site explorer will show you a bit more links (there index fetch every link that has been shared on twitter) where as the largest link index I know are Ahrefs and Majestic SEO.
My advice would be to get the data from all sources, remove the duplicates and then run link detox. Keep a very close look of what link detox says are bad links because no one other than Google know what exactly is a bad links so all others are just using their own formula.
I am sure if you are going to add the link file on “Link Risk” the results might be different from Link Detox.
Just keep a close eye and decide if you want a particular link to be removed.
Planning to remove links? There is a tool that can help you with that www.rmoov.com just give it a try and remove the links that are bad in your eye!
Hope this helps!