It's important that we don't finish the game until we've played 3 Basic Pokmon, which should be an easy mission to complete
There are a couple of ways around it, certainly
To roll the die, you must pay an amount of mana equal to the number of times you've already rolled the die this turn
While Rakdos Charm has a bunch of relevant modes - exiling the graveyard against Dredge and Reanimator, blowing up artifacts against Affinity or Scales - the most important is "each creature deals one damage to its controller." With the help of Sleeper Agent and Forbidden Orchard (combined with whatever creatures our opponent happens to be playing) it's pretty easy for our deck to give our opponent four, six or even more creatures, which turns Rakdos Charm into two mana burn our opponent for four, six or more damage, all at instant speed, which is an absurd deal
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Reconfigure is not an equip ability, and reconfigure costs are not reduced by Bureau Headmaster's last ability