No real way of knowing. It might cause damage in a year, two years, 3yrs, or you might upgrade before it does. It's hard to document something that may be an issue slowly created over time. Things like electromigration tend to happen over time and not immediately. It may result in things like a random error here and there eventually getting worse. How soon that happens and how bad it happens is likely to vary from cpu to cpu just based on normal deviation tolerances during manufacturing.
As die's shrink (65nm, 45nm, 22nm etc) the likelihood somewhat increases. They try to safeguard against it using different techniques but it does become more problematic due to the thinner smaller traces. Between the rate of failure and length of time it takes to fail it's so hard to test that it's often 'guessed' using various laws and algorithms.
https://en.wikipedia.org/wiki/Electromigration
http://www.eetimes.com/document.asp?doc_id=1280370&page_number=4
My guess would be with a die shrink from 22nm to 14nm it's part of the reason intel warns against it, even if they're erring on the side of caution. They don't want to have to replace anymore cpu's than absolutely necessary so they lay out guidelines to reduce risk. Potential risk doesn't mean likely risk but risk none the less. It's up to you if you think it's worth it.
It wouldn't be the end of the world but 'if' it damages your cpu you're out around $240 to replace it. Some may disagree, but ddr4 has been around the same price as ddr3 for awhile now. My personal opinion is saving $40-45 for an 8gb set of ram isn't worth potentially having to replace a $240 cpu.
Edit: Just to comment on what SkittishGaming mentioned, that's part of the problem. The motherboard companies have made skylake compatible ddr3 boards but the potential risk involves the memory controller. In the past when it was part of the motherboard, so long as they guaranteed and warrantied something great. Skylake's memory controller is part of the cpu however so it's not really up to the motherboard manufacturer to say 'sure, it's fine, go ahead'.