Your cheque guarantee card effectively gives you access to an unauthorised overdraft. If the funds are called upon (by the supermarket's bank) before they're actually available, the cheque will be honoured but you might be charged, by your bank, for going into the red. (It would depend upon the terms of your account).
As you state, there's quite a good chance that your funds will arrive in your account before the cheque is presented. However you should be aware that all banks make large profits by hanging onto money (in their own accounts) during the clearing process. If the cheque is presented on Monday, the money could come out of your account straight away. The bank would then use that money, for a few days (earning interest for them), before paying it to the supermarket's account.
However your real problem will be finding a supermarket which accepts cheques. Asda ceased accepting them in 2006. Sainsbury's & Morrison's adopted a similar policy in 2007. Tesco haven't taken cheques since February 2008. Marks & Spencer also ceased taking them last year. Aldi & Lidl have never accepted cheques. My local Co-op (East of England) have recently stopped taking them; it's likely that other Co-ops will have a similar policy.
To the best of my knowledge, the only big supermarket chain which still accepts cheques is Waitrose.
Chris