Lodge payments were always paid directly to you - they didn't go into the fund at all. The new mission "Trial Run" is also paid directly to you.

I always wondered about that though. For trial run it makes sense - you're going alone, without your "regular" team (who don't even know you're doing it), so you get paid for your services as a single runner. But for the other missions - you're effectively getting a "bonus" on the sly. I would have thought that if they found out (and there's one mission where they do), that they'd want a cut...

On that note, I really like the idea of having money deducted not just for the fund, but also the salaries of the other runners and the purchase/replacement of equipment and ammo. It makes the whole thing seem more real IMO. However, doesn't that mean that those other little side missions (e.g. from Gunari, sewers, etc.) are effectively being done for free by the other runners (not including the mercs you pay up-front for)?

It would have been a tad better if those side missions paid higher fees, but then also had deductions for runner pay and the like. It's not a big issue or anything, just seems a bit strange to have runners helping you for free (not including the new "personal" missions, which are done explicitly as favors).