Stage 4, for some reason, had a damage near the end before using the 2nd to last Flame Charge. This damage is removed, 14 frames, but it's not enough for two frame rules. 8 frames intentionally inserted in stage select for lazy-sync.
In Stage 2, with little concern for optimization, I shot a block with a full-charge basic shot. Since we need 140 frames of charging to even hit this block, there's no way to deal with these enemies other than to have a Charge Swap Bubble Barrier already in play. Apparently, hitting the block like this means we can't switch weapons until we shoot once more first, but at least an uncharged shot counts. Two frame rules here, but again, no concern for careful optimization.