You mentioned you could try to switch to a more fulfilling position in your current company but don't know how it would work out. Why don't you give it a try, and if it doesn't work out, then apply to Company B?
Due to timing of hire cycles, if I want to initiate with Company B, I need to do it soon. I could put off until next year, but the more I delay, the less far along I get in the process versus time.
It's really hard to to predict what my future in Company A is without someone else being in that company. A year or so ago I got a new manager. Prior to that I was about to walk. So, when I got the new manager I said "i'll give this guy 6 months to see if he can turn things around, and if not I'll walk". After 6-12 months, the new manager has definitely improved things, but not enough; critical problems remain. Will my current job in Company A improve? Will my manager speed up his changes at all? Who knows, but based on past record it will be slow. Company A is going in the right direction, but so so slowly.
In other groups in Company A, my coworkers are getting the profession experience that I desire. But, switching to their group is quite tricky because my manager might not want to lose me, or the other group might not want me. Beyond this, other groups in Company A are an unknown; I don't know whether there are other good options out there. I am fairly confident that other groups having the level science I am hoping for are low.
Additionally, there remain some critical problems with Company A that can only be changed with changes in leadership, as well as the turn over of past generations and moving forward of new generations. Company B doesn't have these problems, or the other ones mentioned above, but has some tradeoffs such as a more cut-throat environment and less benefits (vacation especially). And these tradeoffs could be major; if I lost vacation time and was able to see my parents less, and their health suddenly declined, I would feel significant regret for the rest of my life for not seeing enough of them during the good years.
What Company B probably does have is a higher caliber of scientist; sometimes I feel like the best way to grow and improve yourself is to put yourself in an environment where people are more talented than yourself. Then in addition to be pushed to improve, I'll have people that can more effectively show me the way. I really don't feel like this is present in Company A.
I feel like trying to predict the future of a company in this regards is like trying to predict the stockmarket (in some ways they are one in the same).
In regards to your question:
I could try to move around my current company (A) first, but I would feel a little guilty if I orchestrated a move and then left the company.
I could also apply to company B, and if they don't accept my negotiations on vacation, then decline the offer. However, the risk is that work of my attempt to work at Company B will reach Company A. This would obviously be unprofessional, but it's always a possibility.