Just to update I was able to change the mode of the IOS58 files via wupclient using the commands @Ryccardo provided
w.chmod("/vol/storage_slccmpt01/title/00000001/0000003a/content/00000000.app", 0x660)
w.chmod("/vol/storage_slccmpt01/title/00000001/0000003a/content/title.tmd", 0x660)...