Hello Yuvraj
Thanks for the question.
It is certainly possible for two SMSFs with, where the members of each SMSF are not related to the members of the other SMSF, to each subscribe for units in a unit trust (UT) such that each SMSF has a 50% interest in the UT, without the investment being an investment in a related party.
Crucial to this is that neither SMSF (and its related parties) have a majority interest (which is a greater than 50% test) and that neither SMSF is capable of exercising what is referred to as sufficient influence in the absence of majority control.
Ifs, as you have described in the question, the corporate trustee is equally owned by the members of each of the two SMSF and that there are an equal number of directors from each family group and that both sets of directors from each SMSF are equally involved in the decision making of the trustee of the UT, then neither SMSF should be capable of exercising sufficient influence.
Partnership concerns
However, I do see a problem if either the members of the respective SMSFs (say a member of SMSF 1 and a member of SMSF 2) and/or their spouses commence a business in a partnership with each other.
This is because we do not want the SMSFs and the members of each SMSF to be Part 8 associates of the members of the other SMSF. This is because if the fund members of SMSF 1 and SMSF 2 are Part 8 associates of each other, the unit trust will be a related party unit trust investment for both SMSFs. Where this is the case, the unit trust would be need to comply with the requirements of Regulations 13.22C and 13.22D to avoid by an investment that is an in-house asset.  Some of these requirements in the relevant regulations are that the unit trust does not have any gearing and if it owns real estate, that the real estate is not leased to a related party unless the real estate is business real property (amongst other requirements).
Section 70B is the SIS Act makes partners of a member of an SMSF Part 8 associates of the SMSF member. Moreover, this will the case whether it is the member of the SMSF that is in the partnership or the spouse of an SMSF member.
Best regards
The Auditors Institute