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The Youth Mobility visa is for young people who want to travel abroad for a short period of time. The intention is for them to experience other countries temporarily. It explicitly says that the period limit is one year.
Your wife's intention is very different, She want to join you in Germany and live there on a permanent basis. The Youth Mobility visa is not appropriate. This is clearly shown by the question you mention, which your wife us unable truthfully to say yes to. She intends to stay longer than a year. It's irrelevant whether the visa could be extended or not.
If your wife does not mark the checkbox she will not be given a Youth Mobility visa. If she does, then she will be suspected, with good reason, of having lied on her form. The repercussions of the latter will be much worse than being denied a visa.
Questions about how to have your wife join you permanently in Germany belong on our Expatriates site.