When using the /teleport command, the entity rotation is changed to south facing.

/teleport @p[r=0] ~ ~ ~3

/teleport @p[r=0] ~ ~ ~3 ~ ~

All relative rotation is adjusted from this south-facing rotation.

/teleport @p[r=0] ~ ~ ~3 ~90 ~

Testing in 1.11.2 and 1.12-pre6, with and without plugins installed. Result is the same.

Tested in 1.12-pre6 vanilla, rotation is not overriden and the command acts as expected.