How do you drain Velveeta Rotini & Cheese with Broccoli, without losing the rehydrated Broccoli?

One option is to line your strainer with cheesecloth, which will keep just about anything from getting through. Since you're only putting pasta, water, and broccoli through it, uou can rinse and re-use the cheesecloth so it's cost effective.

I buy my cheesecloth in bulk at fabric stores, as it's significantly cheaper there than any food-related store I've ever been to.

How are you straining it? A fine mesh strainer certainly won't let rehydrated broccoli through. Depending on the size of the florets, if they are very tiny pieces, perhaps a regular strainer might, but I doubt it. If you are trying the crack the lid method I could see more issues. A strainer should be fine.

I'd rehydrate the broccoli bits separately. Put the pieces and a bit of water (you'll have to figure out how much) into a microwave-safe bowl and cover with plastic wrap. Give it 3 minutes on high power, and your bits should be nicely rehydrated by the steaming.

Then just stir that into your pasta after you've already drained it.

If you're committed to making boxed mac and cheese, I'd recommend just getting the plain kind and a bag of frozen broccoli. The broccoli will be bigger, nicer pieces, and you can just thaw it quickly and add it to your finished mac and cheese to warm through.