You know, I seriously thought I was the only person that got this but I guess not.
Basically, just do exercised that don’t involve pads on your shoulders with heavy weight on it. It’s pushing the seams of your shirt into your flesh so hard that it’s “bruising” in a way. But I’m sure you already knew that.
Personally, I don’t care about the red marks so I keep using the padded standing calf or hacksquat hammerstrength. If it really bothers you that bad, go with a seated calf raise machine, or get under a leg press and just use your toes to flex the weight up and down OR, get under the sqat rack/smith machine, put a 2x4 or something on the ground in front of you to put your toes on and do calf raises that way with the bar just below your traps.
Or you could go with donkey calf raises with a partner:

It is a good one, just don’t know how many guys you want with their nuts pressed against your lower back.
Opinions are going to differ here so I’ll give you my take. Typically, you shouldn’t be doing that much cardio on lifting days because the two nullify each other. On top of that, I don’t know if you’re dropping a shake right after your workout in the gym but with 30 minutes of cardio, you got around another 15 to 30 minutes to get your ass to a quick uptake protein source before you start losing your window of quick nutrient absortion.
If you’re going to run for at least 30 minutes, then I’d wait until your off your lifting days to do it. Or do HIIT because you don’t need to do that for anywhere near 30 minutes if memory serves me correctly. Or just don’t do cardio for 30 minutes after your workout. You say you keep your heartrate up while lifting. If that’s true, I’d finish off my lifting with 10-15 minutes of slow cardio then.