The guards are either too high or too low. When I put them too low the bar still touches my neck if I was to bail out of a lift. When they are 1 hole up the bar doesn't touch my chest (even when I arch my back a bit and inhale, I just started lifting again).
Here's a video illustrating benching in the power cage. He has a pretty high arch but that's the only alternative if the lower safety is indeed too low.
Another option is to do the pin press. It's not a full range movement or a substitute for regular bench press, but it is a nice supplemental exercise which you can rotate with regular bench.
Finally, dumbbell bench press is comparable to barbell and is a lot safer when training by yourself. Also as @MaedeRubenstein mentioned, make sure to keep the bar/dumbbells over your chest. Even when you start failing, just let it come down to your chest. Attempting to throw it back into the hooks might cause you to miss and end up with the bar crushing your neck. If it lands on your chest one technique is just to roll it down to your thighs, and just sit up.
It sounds like the too-low position is right - just touching your neck. I'm assuming that in that spot you can still slide out if you needed to. (In other words, that just touching is not the same as crushing.) With so many different body sizes you're not going to find a 'perfect' fit - as long as the bar doesn't 'crush' your neck you're fine. (And keep the bar over your chest - not neck - when lifting.)
You could try putting a towel or other padding underneath you.