With such a small wedding, and Daphne being the only person the bride has a question about and her being so close to the bride, I would just ask Daphne directly if she plans to bring someone with her. So, essentially, yes, giving her a plus-one, but in a more personal way than just stating it on her invitation with no discussion. Presumably Daphne doesn't have a serious significant other (as she would have told the bride by now), but who knows, it's nice to let her make that decision.
Is the couple worried that Daphne will abuse this privilege somehow, like bring a poorly-behaved flavor-of-the-month to an intimate wedding, or a buddy just looking for free food? It doesn't sound like the kind of occasion that would attract a party animal/wedding crasher type.
As for whether the bride and groom should pay for Daphne's hypothetical guest--I would treat them the same as other similar guests. If the couple are paying for all the other guests, Daphne's friend should be paid for as well, because it would be weird to have literally one person in the whole group treated differently (even if one could make a legit distinction in their status). If there are other cases where the couple are not paying for a particular guest, Daphne's friend might fall into that category.
Why might Daphne's plus-one raise a transportation issue for the couple? Surely the person would just drive with Daphne from the city two hours away. Were the couple planning to buy Daphne a train or plane ticket instead, and wonder if they need to buy the plus-one's as well?