I would be more concerned about getting these guy vigorous than trying to make style decisions about them.
This is correct, you should never cut a Juniper flush you will just wind up with a spot unexplainable on the trunk. Junipers are architecturally isolated meaning that growth lines are specifically associated with branches. You lose the root and growth line you lose the branch you lose the branch you lose the growth line and often the root. So if you cut flush the wound will not heal over as they do on some Pines or deciduous trees, the would just sit there while the tree grows around them. Over the period of many years the trunk may encapsulate the wound but the wound itself will not heal. It will for ever leave the evidence of someone cutting the branch flush. This may not bother you but in the end after years of work and effort you may be unhappy to have that element staring you in the face forcing you to hollow it our and making an Omo of it, of something similar.