Lets also not forget that the Branch in town in Undermanned. Focusing what manpower they have to keep an eye on the MC while Tom escaped and was able to make it to the Church. Don't forget the Goblin Girl wondering around in Town in her human suit proves they are having difficulty noticing things. Lets also not forget there was only 2 Guards at the front of the Church when stakeout scenarios would have at least 4 - 6 making the MC require to do more stuff to fully distract all of em (This is taking into account police and F.B.I. stakeouts).
Speaking of the Main Branch Building and surrounding compound in the Town. While it is true the higher up in the Branch Office would be able to gain special living conditions the lower ranking would require whatever they can get their hands on (when the town is walled off they can have tents, makeshift buildings made, and make use of Trailors) but if the MC was able to purchase any Apartment Complex, Hotel, and Motel he could put a damper on those sleeping arrangements were once maybe 2 Goons may have to share space now they are forced to share with maybe 4 or even 6 sharing the space. That creates problems (Friction and Exhaustion not to mention if any infighting).
Speaking of the Ambush there is also the Ninja group the MC could convince to assist him (they can use the Tunnel to get into the Town). Maybe not be at the ambush but convince them to attack a weakpoint (most likely a structure at one end of the Town) which will force the Branch Leader to send Goons to fix it reducing numbers at the Ambush site. The Goblin Girl could be convinced easily (allowed to set something on fire or possibly blow it up) to destroy an Organization Warehouse in the opposite direction and get out of there (that will also deviate goons from the Ambush site).