Hey David! And welcome to the Click & Grow family.
Your assumptions are right. The use of the second pair of extension arms will leave lower plants with less light and is therefore not recommended. We even removed the second pair from our new packages.
I personally would just guide the tomatoes past the lamp. When tomatoes appear, they usually bend the plant downwards. If you post a picture, maybe I can give better advice.
My plants reached the top time ago and I added the extension arms. But I just added three more pods, so I’m not sure if the new ones are receiving the light they need. After reading this I removed the arms, but in other posts they say it’s not a problem to have them on.
Should I never use the extension arms as you said here, or should I use them?
This set up is totally fine with one pair of arms. This is how it is meant to be used, so you are doing great and it is ok to start new plant pods like this.
But, for the future, also go over plant care tips. You can find these on the web for every plant pod or on the app. e.g. chili peppers require thinning right after sprouting and pollinating to bear fruit.