Freezer bags at altitude?

You should be fine! I don't live at sea level but from 4000 to 13,000 I've never had a problem.

I have always put a pin hole at the top of the plastic bags I use to repackage in. It makes loading a bear canister much easier because you're not having to deal with trapped air. You'll get some expansion on things like candy bars but in my experience I've never had anything expand enough to burst.
As an aside if you want to get into some saving some weight consider not using freezer bags. They weigh about twice as much as a regular bag and though they may seem flimsy I've been using them for cooking in the bag meals for years.

I'm assuming you squish all the air out to get them to pack smaller. Yes they will expand. I've had some pretty tight bags where I just zipped them up full of air. I live at 160' and hike at 8000+'. Reflectix cozies fluff up pretty good too.

"Reflectix coxies fluff up pretty good too."

All the more reason to use a synthetic fleece cozy.

So, if I squish all the air out, and cram them in the bottom of a bear canister where there's no room to expand, do you think they will burst?

I have a vacuum sealer, but then the bags won't conform to the bottom of the bear can as nicely. I wonder if they make bags with those little one way valves on them. Like the ones on coffee bean bags.

I've never had a freezer bag or even a thin sandwich bag pop open up to 11,000 feet. It takes a lot of pressure to pop a freezer bag, far more than air expands in a few thousand feet of altitude. Try sitting on a freezer bag with stuff in it. If you sit down on the bag abruptly enough, the closure will pop open.

Vacuum sealing turns the contents into a hard brick, which you don't want. I try to get as much air out as I can, which works just fine. You can use a straw to remove a little more air.

The problem with a pinhole in the freezer bag is that it also lets air back in and lets water leak out when you rehydrate in the bag. If you're going to put garbage in the used plastic bag, the smell will exit the pinhole into your other food.

When you pack your meals roll them up before sealing and pack rolled. This seems to work better for me.

But no, bags won't pop. They are not like say a bag of chips, already filled with air ;-)

And yes, my FBC cozies don't fluff up at altitude!!

My experience has been different than Mary's. Yes, the bag could leak with a pin hole in it but why turn it upside down? With the pin hole at the top of the bag (and as long as it's not filled to the top with boiling water)there won't be problem, or at least I've never had a problem.
I've never experienced odors from trash getting into my other food. One thing I know that will wreak havoc with food in a canister is instant coffee. I once packed a canister and put in some instant coffee in a baggie and odor permeated everything. It wasn't from a pinhole in the bag–it actually went through the plastic. The next time I carried instant it went in an op-sak.
There are probably other foods that can be a problem–I just went on a trip with someone who related a story about smell contamination in a canister. I think it was from dried mangoes. I recommend if you have any questionable foods that might cause odor problems pack some up with other food and let it set in your canister for few days.

Dog food will really smell up the rest of your food and/or the dog's pack. If I can smell it through a freezer bag, I'm quite sure a bear will! I put each day's dog food in a freezer bag and divide the freezer bags among two smaller OP sacks (one for each side of the dog's pack). At night they go in my Ursack (or canister, but I haven't actually taken the dog where I need a canister) inside their own OP sacks. My own food is in another OP sack. I don't know how well the OP sacks work, but at least my food doesn't smell like dog kibble, and my dog can't detect the odor through the OP sack.

I did the pinhole thing, keeping the hole right next to the zip so it wouldn't be a leak problem when rehydrating, and it worked great. Definitely helped me squash that last bit of food into the bearikade, and no leak issues.