The Nintendo DSi has two sets of wireless memory slots for WiFi usage in the Settings. The first three slots you're shown are the slots that support WPA 1/2. A separate submenu shows the other three slots, which are the WEP or open security slots. The first three slots are used for DSi-enhanced games, and the last three slots are used for regular DS games.
Pokemon Black Version, White Version, and Black 2 and White 2, are known as what are called "DSi-enhanced" games. They support the WPA 1/2 protocol when loaded on a Nintendo DSi. As a result, when loaded on a Nintendo 3DS using an up-to-date version of TwilightMenu++, nds-bootstrap is able to let the DSi-enhanced ROMs for these four games detect the Nintendo 3DS's regular internet settings instead of falling back to the DS mode communications settings, so long as WiFi is enabled in TwilightMenu++'s settings.
You have to load them specifically through nds-bootstrap via TwilightMenu++ to do so; you have to have WiFi enabled in TwilightMenu++'s settings; you have to have a WiFi profile set up in the Nintendo 3DS's system settings that is a WPA 1/2 secured access point in order to do so; it's preferred not to have a DS-mode communications profile set up at the same time, as it may cause that fallback mentioned previously.
You're arguing with the primary developer of TwilightMenu++ on this, the man should know how his own homebrew application works in addition to any bugs or issues that may crop up in its usage.