I believe that the artifacts the OP was hearing were in fact due to some parameter being changed between snapshots, quite possibly on his delay; not the output block level. It is perfectly ok to change the level between snapshots using the output block. Several of my presets use this approach. As a matter of fact, it is the best place to do it if you want to ensure that you do not change the level going to, for example, an effect block downstream. Level changes made earlier in your signal chain can change the response of an effect downstream and hence your tone, not just the amplitude of your overall signal. So, for the most transparent volume changes, barring any tonal changes due to the actual increase/decrease in volume (Fletcher-Munson), an output block is probably the best way to go.
Also, as @codamedia alluded to, it is a great way to save on using an extra block. With the Helix I often use a volume block and also a gain block as he does. I place the volume block right before delay and reverb so that I don't cut off my trails if I depress my expression pedal fully heel-down (0%).