Are the addresses safe to use now?
They were always safe to use as long as you know what you do.
Should I use your method instead of mine?
Yes
Is it certain that, if I for any reason need to use the seed to restore the wallet, I can use the addresses again if I increase the gap limit as per your or my method?
Just try it. You can have multiple wallets open in parallel.
Create a new wallet under a different name (e.g. wallet_1).
Use the same seed as you used in the default wallet.
Set the gap limit to 200 and restart electrum.
You should now have the same addresses in both wallets.
If so you are good.
If not then your seed is most probably wrong.