The plot hole is that V and Panam never talk about it beforehand. That's the issue. Why would V not ask Panam about the text before heading to Embers? Or on the rooftop over the phone? It doesn't make any sense.
In the message, Panam (if I remember), say something like "I can't tell you more at the moment".
When V goes to the Embers, it's simply for talking to Hanako (the "point of no return" message doesn't count here^^) and nothing more. Nothing is really planned at this moment ("much to Johnny's dismay") and even less to thing he/she have to decide something "soon" or "just after".
And also it's Johnny who "drive" V to Viktor for avoiding a "flatline in a gutter".
In short, in my point of view, before the roof, V doesn't plan/decide anything. V is a little forced to make a decision on the roof by force of circumstances
On the roof :
- First call, V can't say anything, because Panam... don't let V talk.
- Second call, assault Arasaka to reach Mikoshi certainly through Panam's "previous plan" in the trash for sure.
Edit :
I'm not sure it's very "clear" what I wrote
In short, until the "fatal" crisis in the elevator (and therefore the roof), V still thinks he/she have enough/more time to choose and decide what to do (in view of the dialogue with Johnny). And that while Panam's plan (on her message) may help him/her, it won't save his/her life. She isn't aware about Mikoshi, Alt, Arasaka,... So there is no way she was able to find a "miraculous" solution in middle of her camp (even with all the goodwill in the world).