Does Superstream affect all contributions and benefit transfers and rollovers involving SMSFs?

In short, no.

Superstream will not apply to member contributions, spouse contributions and third party contributions.

Superstream will also not apply to:

(a)    related party employer contributions;
(b)    Government Contributions (ie contributions made under the Superannuation Government Co-contribution for Low Income Earners Act);
(c)    payments made by the ATO under the Superannuation Guarantee (Administration) Act;
(d)    rollovers and benefit transfers to retail and industry funds; and
(e)    rollovers and benefit transfer from or to other SMSFs.