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That is not a bug. If you went to a block before the amp, changed it to mono, you get the default settings of that block. You are choosing a "fresh" block in place of the one you had. 

You could have the tremolo on all the time, then make the mix sweep from 0-100%, maybe on a parallel path. 

Check global settings>preferences>snapshot edits. You may have to set that to "discard"

Yes. Any parameter you want to change with the expression just hold down the knob, set which expression you want to assign it to, then set the max and min. I control about 6 different parameters with one of my expressions. Don't forget, the min value can be larger than the max value to give it a reverse sweep. I do this when I increase amp gain, I also decrease channel volume simultaneously. 

Set up path 1 with a clean amp and whatever else you want in that path. Then on path 2 set up a completely different amp that is overdriven, with whatever other effects you want. Set both paths with the guitar input, and the same outputs. Now you are playing both at the same time. 

Cool. Be sure to mark you post as "answered" so someone may find the same fix if needed. 

The stock cab/IR models on Helix are very good, but like everything else, some players prefer 3rd party IRs. Yes, IRs are wav files.  24 bit, 48 kHz, 1024/2048 sample IRs are compatible with Helix. 

I play primarily strats and teles. I get no "digital sounding" guitar input and use my volume pot on the guitar all the time for controlling input to the Helix. In my experience, using my guitar volume pot on Helix reacts the same as any "real" amp I have ever played. 
 
What you are describing is highly dependent on your pickups, signal chain, the effects you have in your preset, the order of effects, and the amp model you are using. If I use the noise gate on the input block, I have it set to very sensitive (-70 to -60dB), but most of the time I have it off. I have input pad off so I don't prematurely cut the input signal. If you have a compressor in your chain, your volume pot response will be affected greatly. Some gain/distortion/fuzz pedals react quite differently to changing volume pot because of the compressing of the signal that they do.
 
So test this theory, set input pad off, noise gate off, drop in a Plexi amp/cab block with no effects and default settings. Plug in your strat on the neck pickup and roll your volume pot around. It should be reacting just like the real amp. On 10 it should be pretty crunchy, getting down to 5 and below, it should be cleaning up very nicely. 

You can route USB 1/2 (your audio playback) to the XLRs (in global settings) and route your bass to the 1/4" out (in your bass preset). 

You don't have to insert a Y in the lower path. You just put the cursor on the delay on the lower path, hit the action button, then move the delay down with the joystick. It creates the parallel path for you. You may have to adjust the split and merge, but you just put the cursor on them, hit action, and move them where you want. 

I am not at my Helix now, but there is also a parameter called "intensity" or something like that. Turning that up higher will generate some tones that are a bit "off" to get a more spooky sound. Like mentioned above, put Octo (and particle) verb in a parallel path so that you have some tone that is unaffected. That will help. Turn that parameter down some too, that will help. 

move the cursor over to the volume block. Hold down the "Position" button below the screen. The menu will appear that will allow you to choose which expression pedal. 
 
If you choose EXP1, you may get the pedal position going to 1% randomly. EXP2 is default. 

Change all of your volume blocks to be controlled by EXP2, not EXP1. EXP2 is default, and you won't see the volume drop issue.