I stuff all empty containers full of stuff.
If I don't do that then I am just packing empty air around.
I like things like Nalgene lab bottles for anything that can be squeezed and leak.
Toothpaste is nasty to clean out of your pack once the tube has ruptured.
I just try to avoid putting toxics into food containers.
Neither matches nor hand sanitizer are toxic, but they can be stuffed inside of a baggy first if you are worried about them.

Where are you going to put your water?

I think some people see those water bottle "Survival" kits in various stores and simply try to copy it. Or they may just buy one. Truth is, if you're in a survival situation, water is one of the most important things you should have.

Keep your water bottle full of water. You'll be happy you did when you need it.

I think it is a good idea to put the stuff in the bottle. If you get a source of water to fill the bottle, you can always give the bottle a decent washing first with clean/boiled water.

I echo the comments of adding a small waterproof bag of some sort folded into the bottle. Maybe include a small stuffbag as well. They don't take up much room. Then, if you need the bottle, you will have your items in a waterproof bag inside the stuffbag, which can be placed where you need it or carried in a cargo pocket, or what-have-you.

In most survival situations, I need water more than I need my survival stuff. After an earthquake, there may be no opportunity to turn on a tap or filter water from a lake for a cold refreshing drink - my nearby lake should be polluted by ruptures to regional sewer lines. To be prepared I need water stored before an event, and not hope to find it after. So stuff that I might store in a nalgene I just store elsewhere. Smelly stuff that attracts critters and bears do just fine in a bear bag, hung from a tree at night.

And if you use one of the SS type bottles for your kit container, you can boil your water in the bottle, if need be. Not as easy to do with a poly bottle.

All depends on your need for that bottle. As Lono stated, you may want it filled already, or you have it as additional carry capacity if you source water.

Who says you only get to have one water bottle? My water goes in a different bottle (or hydration bladder) than my survival gear. The survival bottle could be pressed into use as a water holding implement during an emergency, but normally it's just a watertight container for survival gear. It does not hold my only survival gear. It supplements the PSK that is always in my pocket. But you can get a lot more survival gear into a Nalgene than into an Altoid tin, so the Nalgene stays in my pack.

Zip Lock bags simply do not work for any period of hiking.

I tried them out in my water backpack which is what I use to hike along the lake and river and has the chance of getting splashed or wet.

After maybe 5 miles the bags were rubbed through in some places, and others had opened. Double bagged, and not, zip-lock brand heavy duty and normal.

Bags simply are not strong enough to move around in a backpack.

They have THICKER plastic bags not sold at grocery stores that work... the map carriers that are for hiking are nice too.

I store stuff in my nalgene, works great.

I have other water in the backpack, so it doesn't need to reside in the Nalgene bottle right now. The Nalgene bottle (and it's contents) are for a survival situation, so I'm not concerned about having to remove the stuff to use the bottle.

There's water everywhere here, I doubt I'd have a hard time sourcing any. And I bet my odds are better of winning the lottery every week for a year straight than of having an earthquake hit here.

I'm also not too worried about the stuff that I'm now carrying in the Nalgene bottle getting wet when I take it out. Most of it is a waterproof flashlight, a Fox 40 whistle, a knife sharpener, a magnesium fire starter, a wire saw, a Starflash signal mirror, a waterproof match safe, etc... I'm just trying to conserve space by not having to take up space in other parts of the bag. In my opinion, anything in my bag that can contain something inside of it, should do so to conserve space.

So long as you have a second water container, or something to put the stuff in if you need the bottle, I say go for it. A good polycarb is hard to break, is water tight, and just can't die. A coworker of mine kayaks, and it turns out he keeps a 14oz wide mouth full of firestarting gear, PA tabs, SAK and a few odds and ends in a pocket in his life jacket and tethered to him in case he and the kayak have a parting of ways.