It takes a tick longer for a command block chain to stop being powered once the power is removed. This is the case both when a redstone block is removed, and when NBT auto: 0b is used. (I cannot verify that this extra tick also occurs when the block is powered as well or not.)

The problem with this is that it can throw off things when, for example, a button is meant to stop another command block chain from incrementing a score, and then assign the value of the score to another score when the first score stops changing.

To Recreate the Problem

1. Create and display to the screen an objective named "tempObjective"

2. Place a repeating command block that needs redstone power containing the command:

/scoreboard players add X tempObjective 1

3. Place an impulse block separately that needs redstone power, has a button on it, and will replace a (future) redstone block next to the repeating command block with air.

4. Add a chain command block to the impulse block which holds the command:

/scoreboard players operation Z tempObjective = X tempObjective

5. Place the redstone block next to the repeating command block, wait a second, and then press the button on the impulse command block.

Result

X will be greater than Z.