Don't kick player from Bungeecord when using MCAP. Only thing is that kick message should include "whitelist" (so, whitelisted, whitelist, whitelisting works too)
MCAP is Spigot plugin for whitelist integration with Discord and whitelist by nicknames: https://www.spigotmc.org/resources/mcap.100381/
Contact me at Discord: Stopper#1631 if you have any problems.