So I took my new toy to the Twelve Apostles a couple of weeks ago. I was a bit silly and left the ISO so high, as I forgot to change it from a previous session, hence some of my photos are obviously crazily overly exposed. Not to worrry I say, I'll edit them afterwards. Whilst they show up in the Nikon program (ViewNX) as I've adjusted them, windows programs can't read them how I've actually edited them. They're in RAW, I imagine it's somehing to do with that....
I use pentax and oly so im not familiar with Nikon raw editing software, but there must be an option once you have edited to "save image". Somewhere in that you should be able to select the format of the saved image. Saving as a Jpeg should allow virtually any software to "see" the pic. Saving as a Tiff file, or an NEF file or a dng file will limit your viewing and printing options. It will also result in larger files on your storage.
Adjustable Iso is a godsend but you've stumbled on one of the traps, lol. That said, the camera should adjust and avoid over exposure unless you hit one crucial point - exceeding the maximum shutter speed of the camera. This can happen with camera's that are restricted to 1/4000 (or less) and big lens apertures / high iso.
Check your camera's maximum shutter speed and then check the files to see the shutter speed used. If its at maximum then the overexposure is probably due to that. If its less than maximum then the metering has done something unexpected. Spot metering, pointed at a shadow area for instance, can blow out any sky in the pics.
Edit: just checked, your D3300 has max shutter of 1/4000 of a second. A bright day and really high iso could require faster than this. Check your manual and turn on "highlight warning". When you review the shot on the lcd, areas close to over exposed will flash and give you a warning that something may not be quite right.