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I would not call it “pairing”. I call it “connect ledger to a front-end” (like MetaMask etc).
When you do that, the front end will not use its internal seed, instead it will use the seed of your ledger, so it will give you access to your ledger accounts, and each transaction from those accounts will have to be approved on your ledger device (because they will be signed by your ledger device).
This is 100% safe, as long as you NEVER enter your ledger seed phrase in another front-end (you should ALWAYS connect the front-end to the ledger, that’s the only save way).