My personal answer (and something I personally believe most DCC funnels do NOT do well) is that you should especially consider the IMPACT the funnel will have on surviving characters. A funnel is an amazing time to give the players crazy mutations, powers, or even just hooks to other things you want to come up later, after the funnel. Due to the fragility and unattached attitude players will have, you can get away with really warping a character into something interesting. For example, I ran a funnel of my own creation for a group of players. One of the characters touched a pedestal with their bare hand, which jammed a long rod of alien metal into their arm, which allowed them to use their arm as a weapon but also allowed aliens to control it (think Magneto controlling Wolverine's metal bones but just the arm).
To your secondary question, "I'm especially concerned with how to account for the added burden on players to keep track of multiple characters", I think that there are two things to keep in mind:
(1): Traditional roleplaying will normally be heavily mitigated. I've seen this go one of two ways. Either the players each choose one character at a time to put to the forefront for roleplaying, or they just don't really talk in-character. This is generally expected for most traditional funnels. A funnel is very "meta", and strategic thinking is encouraged, often involving some metagaming, especially since (A) the players can't really get into character with three characters at once and (B) the players might not even get the chance to fully get into character due a character's unfortunate demise
(2): Players often (at least effectively) play as one character with two hirelings at their personal control and disposal. So, when thinking about the burden a player may have, they'll often come up with some solution by themselves or as a group to mitigate the issue. Mechanics might be an issue, but if you're running something rules-light, it normally isn't an issue. When designing a funnel, at least the one's I've seen (I haven't designed one yet), traditional OSR problems usually do the trick, although you are expected and encouraged to make the stakes a LOT higher, or the problem a lot harder to solve, at least without some collateral damage.
Hopefully all that helps! Let me know if you have any additional questions!