Yes, is caused by that, background always using the default container.
This can be solved with webRequest.onBeforeSendHeaders as described here

Here's the PoC for toolbox.

Set up listeners to update the container we're using and the headers of the requests if needed.
The custom header tmp-source was included since otherwise this would update all requests, not only the ones from toolbox.

let storeId = '';

browser.webRequest.onBeforeSendHeaders.addListener(
	async (args) => {
		if (!args.requestHeaders) return args;
		let source = args.requestHeaders.find(value => value.name === 'tmp-source');
		if (!source || source.value !== 'extension') return args;

		let cookies = await browser.cookies.getAll({
			domain: 'reddit.com',
			storeId: storeId
		});
		let cookiesMap = cookies.map(value => `${value.name}=${value.value}`);
		const requestHeaders = 
			args.requestHeaders.filter((header) => {
				return header.name !== 'tmp-source' &&
					header.name !== 'Cookie';
			})
			.concat({
				name: 'Cookie',
				value: cookiesMap.join(';'),
			});
		args.requestHeaders = requestHeaders;
		return args;
	},
	{ urls: [`https://*.reddit.com/*`] },
	['blocking', 'requestHeaders'],
);
browser.tabs.onActivated.addListener(async (arg) => {
	let tab = await browser.tabs.get(arg.tabId);
	storeId = tab.cookieStoreId;
});

The only difference when making a request is to include our custom header in fetchOptions as a flag to replace the headers

async function makeRequest() {
	const fetchOptions: RequestInit = {
		credentials: 'include', // required for cookies to be sent
		redirect: 'error', // prevents strange reddit API shenanigans
		method: 'GET',
		cache: 'no-store',
		headers: [
			['tmp-source', 'extension']
		]
	};
	let url = 'https://old.reddit.com/subreddits/mine/moderator.json';
	let res = await fetch(url, fetchOptions);
}

Now, this won't play nice with the cache, I quickly saw that window._TBCore is used as well as localStorage, so those need to be updated to take in mind the cookieStoreId.

Firefox container storage weirdness #98

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