I've come to think that this is somewhat by design.

I don't think SE really wants us manually using every embrace (or embrace at all really).

Sure, it would be nice if they let us, but, there is actually a pretty soild work around: Fairy placement.

Your fairy has a short auto cast range for party members at a bout half her max cast range (will auto cast on you at max range though).

So place your fairy accordingly. Eos has a pretty solid reaction time for casting embrace on targets, so keep her near only those targets you want her healing and she will heal them when ever you would other wise tell her too.

For titan: Leave her on follow and keep yoruself near the middle.
AK: Place in side ark of boss (will heal tank and any mele, ranged shoudln't need her help)
CM: Auto follow and keep near tanks and dds. (There is no boss aoe that isnt' easy to avoid)
Coil 1: Place in side arc on side bards aren't bringing slimes in on.
Coil 2: Auto follow with you in the front middle position will hit tanks ( a little vague, lots of different strats being used for this fight so, YMMV)
I haven't personally healed 4, so idk, my bff jill, but having tanked it I feel there are viable options.

TL, DR: Place command IS your manual targeting of embrace command.