If the siphon was supplied with the cistern it should fit unless you have fitted it wrong.otherwise you need a different siphon. Ie one with cord to push button
Can't see what else you can do. The location of the valve is dictated by the hole in the bottom of cistern. Even turning the valve throgh 180 deg. looks like it will make the situation worse.
I would contact the supplier, and see what they can do for you. Cable controlled looks like your only option if you're keeping it.
I once had this problem with one of those B&Queue to go toilets. I found that the base of the cistern was not manufactured perpendicular to the sides so the valve was misaligned at the top.
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