Not all rental companies allow driving cross-borders. If they do, there will be a surcharge for every day of your rental. It will not be obvious from your quote, that you require the cross-border privilege. Therefore, you need to ask that specific info from each rental company.
I have driven in Slovenia a couple of years ago. At that time, the best available deal was in nearby Austria -- even considering the cross-border surcharges. That trip worked out beautifully.

One tip about driving in Slovenia: many roads have tolls. It's best to prepay the tolls by buying a sticker ("vignette") at any gas station. Otherwise, the charges will be much higher.