There is absolutely no harm in doing this.
sitecore_master_index root is set to
/sitecore and all the other indexes which operates on
master database have their roots set to one of the
/sitecore item descendants. It works just fine.
You can create another index with
/sitecore as a root without any issues.
I can imagine having a bucket with different type of items in it and having multiple indexes with their root set to the bucket root, one of the indexing only items which use templateA and another indexing only another template.
Question is: "is it worth to maintain 2 indexes instead of having 1 index and then getting what you want from the index using more specific queries?". But the answer is "it depends" and this may a very good solution in your scenario.