No, if you use em3, the group will not be applied to that interface.
This configuration should be a safety measure to make sure that you don't apply the group to other interfaces that you don't want to by mistake.
Check this quick test:
{master:0}[edit]
root@EX4200# show interfaces ge-0/0/1
apply-groups TEST;
{master:0}[edit]
root@EX4200# show interfaces ge-0/0/2
apply-groups TEST;
{master:0}[edit]
root@EX4200# show interfaces ge-0/0/3
apply-groups TEST;
{master:0}[edit]
root@EX4200# show groups TEST
interfaces {
"<ge-0/0/[12]>" {
mtu 6789;
}
}
{master:0}[edit]
root@EX4200# show interfaces ge-0/0/1 | display inheritance
##
## '6789' was inherited from group 'TEST'
##
mtu 6789;
{master:0}[edit]
root@EX4200# show interfaces ge-0/0/2 | display inheritance
##
## '6789' was inherited from group 'TEST'
##
mtu 6789;
{master:0}[edit]
root@EX4200# show interfaces ge-0/0/3 | display inheritance
{master:0}[edit]
root@EX4200#
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