That makes absolutely no sense but I just tested it myself and you're absolutely right. I think if it were me, I'd be booking VIE-ATH and ATH-JKH as two separate tickets being that the layover is so long. You should be pretty safe with 7 hours in my opinion. Of course, that's assuming that it doesn't increase the price drastically?

I have used expedia for A3 flights in the past and they were fine. I even used upgrade coupons without any problem on that booking. I'm not sure whether they give you all of A3's various fare options these days though, as it's many years since I used them. That was for TXL-ATH-LHR-ATH-TXL, which the A3 website wouldn't sell me either but I can understand why.

Your only other option as far as I can see is to ring them up to book. They should waive the call centre fee if you ask me, as it's clearly their website error stopping you booking online but I know getting A3 to waive that fee tends to be very difficult. At least by ringing up you would highlight the problem to them and maybe someone would get round to fixing it.

Good luck and do let us know how you end up solving this one.