Generally counter-phrases can be used adverbially. As for 一つ in the sentence, that's why.
So it can be 三つ500円, too.
As for に vs で, に is more felt like ratio, i.e., 'per' whereas で more like 'adding up' (translationwise, it can be the usual with - with three of them,..).
Accordingly, 一年に一万円 sounds like '10000yen per year' = recurring 10000 yen (losing or getting); 一年で一万円 sounds like the resulting (cost or gain) 10000 yen after a year, not necessarily recurring. Of course, if the contexts make clear, both are interchangeable to some extent.
The choice of に/で also depends on the verb. If a counter-phrase is an indirect object, only に can be used:
- 一人に一万円渡した
- ?一人で一万円渡した (This means, if anything, I handed 10000 yen alone)
In the sentences in question, the counter-phrases are subjects and に cannot be used: 一つに200円です won't work in that context. (Note that 一つに200円かかりました would be fine since かかる can take に-phrase.)