Current models of drone are pricey,although JD says the cost will  gradully come down as it scales up the network and bulids more drones (it plans to sell those it makes to other firms,as well as use them for its operations).

1 as well as 前面的逗号可以去掉么？

可以省略这个逗号。as well as为准并列连词，并列作宾语的不定式to sell和（to) use。不过，as well as并列的A、B二项中，强调A项。A as well as B, 等于not only B, but also A.

2 those it，those 指代drones it 指代哪个呢？those和it之间是不是省略了什么？

it指代JD（公司名）。it 前省略了引导定语从句的关系代词which/that（在从句中作宾语）。