At a high level the changes you are making are required to power the board from a 3.7V battery, however after you make the changes you will run into a host of other problems.
1) There will be no 5V supply on the board, hence the HDMI output, and the USB ports will not work, also any mezzanine cards that require 5V will not work. This might be acceptable depending on your use case.
2) The charger in the PMIC needs to be programmed to charge the battery you have attached, and measure the battery temperature with a thermistor in the battery pack. The charge rates need to be tuned to the specific battery chemistry, temperature, and capacity that you are using. These rates are not reprogrammable in the open source SW. Hence you may cause your battery to over charge, or charge too fast causing a fire. This is one of the reasons we elected to not support 3.7V batteries. (the other reason being the added cost of a 3.7V to 5V boost circuit that the majority of users would never need).
The 'correct' solution to running the 410c on batteries is to use an external battery pack and charger. You can use a 7.2V (or 9.6V, 11.1V, 12V, or 14.4v) battery pack since the 410c will operate as low as 6.5V. You don't need to connect the battery pack to the barrel connector, you can connect it directly to the Low-speed connector.
Full Disclosure: I am an employee of Qualcomm Canada, any opinions I may have expressed in this or any other post may not reflect the opinions of my employer.