Covering up excessive clicking can be tough.
The basic strategy is to try to reduce the usage and/or frequency of any commands and tables, as these can increase ticking noises and instead rely on instrument settings as much as possible. This doesn't reduce the clicking at the beginning/end of notes unless if you're using commands at that time, but reducing clicking overall makes it less noticable.
Another thing you can do is to try to decrease the resolution of waveforms, because even with silky wave you still get a little bit of clicking when the waveform changes. Again, this won't reduce clicking at the beginning/end of a sound but it helps overall.
Another thing is, as said above, when a whole track is playing it blends in, so if you try to make your track a little more layered that can help. Every little bit helps.
I know those options are not great, but that is part of the challenge. Do not feel bad about removing noise in post production, and when you play live no one will notice. The dirty secret is that a lot of people do it. Recording in the BGB emulator can help because it separates channels, so you can remove noise in each channel appropriately.
There's one more strategy which I don't see people talk about, which is a little counter intuitive. If you use the noise channel a tiny bit in such a way that blends with the clicking and the sound itself, you can actually make it sound less noisy overall. This is what I did with the chord sound at the very beginning of ULTRAACID XX: https://soundcloud.com/dotexechiptune/ultraacid-xx - The chord notes make tons of clicking on their own since it's two pulse sounds with envelopes on top of a full resolution wave channel sound with nothing else playing. I added a small noise channel tone on top of each chord note that ends just after the chord notes, and just tweaked it until you could barely hear the noise tone in isolation but it dramatically decreased the percieved clicking. There is still some noise but the sound was incredibly bad before. There is no post-processing beyond amplification. I think you could even get it to sound better than this because there is some additional noise I didn't hear on my headphones when I first made the track and I didn't explore this strategy much. This strategy is situational and difficult but I hope it helps.