I'm not an expert, but:
1. Either the HO has sent the passport to the In-country team even though you did not fill out the FLR yet. This could mean that either the in-country team will send the passport back and ask you to fill out the FLR yourself and re-send it, or they will process it as in the old days (however I cannot see why they would do this since their rules have clearly changed, so don't count on this).
2. The HO is simply taking its time in returning the passport, and given it did not include it together with the WP letter, wait one more week and then call them up.
Anyhow, you will almost certainly have to fill out the FLR and pay the appropriate fee (unless exempt or company sponsors). Also, in any case, once they get the passport and everything is ok, it will take 5 weeks for them to stamp it (unless they sort temselves out soon and reduce the time; it's getting a bit ridiculous given the amount that one pays for their service).
I am not sure about whether this can be sped up. Your employer could always try and contact the in-country team and ask for some sort of urgent treatment (like if you need to start asap or travel on company business, similar to what HSMP people try), but I doubt it will help much as everyone would do it then.
In any case, you should not worry: given that the WP is approved (this is the main thing), getting the LTR is more of a formality (assuming your immigration records are clean and you didn't use public funds).
The moderators appear to be away on holiday so check again in a while in case any of them has any ideas on the matter.
