That doesn't seem any easier to work with. You're right that the query itself is shorter because you can add the values you are looking for rather than enumerate them. However, if you have 30 bitwise flags you certainly won't be working with numbers like 126. 2^30 is 1073741824. Using bigint, once you've hit 62 flags, that is the highest number of bitwise flags you can have and store them all together and you're reaching the limit and using up a 64-bit int.
Secondly, an embedded array can be indexed by MongoDB. So by using arrays you won't be limited in the number of possible values or the size of int/bigint AND your query can use an index and be very fast. It's also easier to manage because you don't have to convert your flags to their bit position. The only disadvantage is a longer query, which i'd say is trivial.