We have mentioned that the LDS Church has lost its rights to the Priesthood of God as a collective body, but individuals may maintain a connection to heaven if they consistently qualify themselves in the Lord’s eyes. (See posts here and here).
Those who baptize as representatives of the LDS Church have common consent to use their priesthood within an LDS Church setting, so if they are properly ordained (see here and read the comments on the post here) and follow the Lord’s instructions (see here) while ignoring the LDS Handbook of Instructions when it contradicts the scriptures, (as Boyd K. Packer admonished in the training meeting on the handbook –see 2010 Worldwide Training Meeting – Concluding Remarks, and as our Lord and Savior showed by his example against the Pharisees of his day –see Matthew 23), then you can be confident the Lord will acknowledge such faith, even within an LDS setting, and signs will follow those that believe (see Ether 4:18).
For example, missionaries (or those who baptize) should not make baptism dependent on answering the question “Do you believe that [current Church President] is a prophet of God?” (Preach My Gospel Manual, pp. 203-212). See our post here and the post entitled “Baptism is Mandatory” here. Otherwise, the scriptures make it very clear that “anything more or less than this cometh of evil” (see 3 Nephi 11:40), with “this” referring to the doctrine of Christ, requiring only believing in Him and repenting of your sins to be qualified to be baptized (see post here).