Investigate config and app toml override logic

[linear]

Rationale

Chorus One validator as well as one other claim that some of the configs such as peer values are getting overwritten. https://discord.com/channels/798583171548840026/842550346865180682/1223060434056253514

This should not occur, there are only a handful of items that should get changed, and peers is not one of them

DoD

• Create a README with values expected to be overwritten

• Recreate the scenario, showing that other values such as peers do in fact get overwritten

• Change logic so that the only values getting overwritten are the ones in the README to the expected values

[czarcas7ic]

I am unable to replicate this, I am asking Mateusz from Chorus One to attempt to replicate it as he is the one that originally reported it. If he is unable to I will close this issue.