The concept of using 'miswak' was simply to clean ones teeth/mouth. As in the days of Prophet Muhammad (Peace be upon him) there was no tooth-paste, so the best option used by the Prophet - Peace be upon him - was to use any thing to brush his tooth and the best available thing, in his opinion was 'miswak'. So using 'miswak' is sunnah of the Prophet - Peace be upon him. Miswak has not doubt some chemical cleansing and antibiotic effects.
So if any body uses 'miswak' as 'sunnah' then certainly he will be additionally rewarded. But if some one brushes his teeth with a paste, he will also be rewarded for following the 'sunnah' for keeping his teeth/mouth clean.
Regarding equality of reward, it is Allah to decide not us.
Allah knows the best.