If you are talking about buying direct from IB rather than a 3rd party, there is not much risk, though possible there will be some operational inconvenience. Codeshare partners often price the same flight differently, so no issue there. If the price on Skyscanner is from a 3rd party, it may not be live pricing and you won’t know until you try to book if that fare is really available.

You might have issues between the systems with things like seat selection (though I find more problems with this when booking IB metal on a BA code) or OLCI, but nothing insurmountable. If you collect Avios and TPs, you will almost certainly find that an IB codeshare on a BA operated flight will not credit automatically to BAEC, you’ll need to do a retrospective claim. The number of Avios credited may also be different on an IB code.

There may may be a couple of other things that I’ve overlooked and others can add, but in general, if the lower fare exists to book, I would say go for it.