Rechargeable batteries for memory/RTC backup power isn't a good solution today. The batteries will eventually die due to the many charge/discharge cycles that it can be put through. And many rechargeables will self-discharge in a month or two. There are also regulations regarding the metals in these batteries that might come into play.
Non-rechargeable lithium batteries can have a lifespan of 10+ years in a RTC/memory backup use case. This is often longer than the expected life of the product it is in. So, it has become common to see these batteries soldered down to a PCB-- because it's more rugged than a battery holder and it is never expected to be replaced. Of course, this makes many people nervous. These batteries also have the regulatory issues common with the rechargeables.
Supercaps are a nice alternative. They are not always cheaper than the non-rechargeable lithiums, and don't operate as long on a charge as the rechargeables. But they are maintenance free and don't have the regulatory issues.
So, none of the solutions are a perfect mix of cost, regulatory, lifespan, and maintenance free. The designers of a product just have to weigh the pro's and con's and pick the one that they like best.
BTW: One product I did used a Supercap as an RTC backup. It would run about 9 months before loosing it's charge. Of course, turning on the unit would recharge that cap in about a minute.