Every time i try to link my battle.net account to my existing XBOX based bungie.net account, i cannot play on my PC & Console at the same time. I am not trying to play cross platform, but my wife likes to play the console and I purchased the game to play at work on the PC (I know that sounds bad).
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Please note that linking your accounts has absolutely nothing to do with your accounts, themselves. Your accounts are entirely separate from each other, meaning your Xbox account and your Battle.net account are entirely separate; data, licenses, and everything else don't crossover between them, and having one, the other, or both attached to Bungie.net does nothing except attach them to Bungie.net Having them connected to Bungie.net wouldn't keep you from logging in to Destiny 2 on PC and console. Please do note that if you're attempting to play on both at the same time in the same household may cause an issue if your internet connection has problems or if your network isn't set up properly.