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Yes, specifically — several parts of Nitro exist only for Journal3. Its inline theme CSS, 350-450 KB of <style> in the head of every page and inside every cached copy of every page, can be lifted out into cached files. Its filter, facet and product read models get their own result cache, because their NOW() price subqueries make the generic query cache skip them. And the per-device cache carries a shim so a page rendered for one phone is not served to another with the wrong browser classes baked in.

Per-Device Cache is turned on for you when Nitro is installed on a store that has Journal3, because Journal renders different HTML per device on the server and a shared cached page would send a phone the desktop markup. Leave it on. Journal3 CSS to Files is the other one worth turning on, since it takes Journal's inline theme CSS out of every page — but check the storefront afterwards, as it is the one Journal-specific rewrite that touches how the page is styled. Nothing else needs changing.

Yes. Nitro patches Journal3's own clearCache() so that pressing Journal's Clear Cache also flushes Nitro's page cache, query cache and generated assets — you never have to clear both. It is an ocmod patch, so like the rest of them it starts working once you have pressed Refresh under Extensions → Modifications.

No. Journal3 is one theme Nitro knows especially well, not a requirement. Everything else — the full-page cache, the query cache, the firewall, image and asset work, the warmer and the database tools — works on the default theme and on any other OpenCart 3 theme. The Journal-specific patches are marked optional in the modification file, so on a store without Journal3 they are simply skipped.