As far as I can tell the planning minima are the same, its their allowable location and terms of use that are different.
A 3% ERA can be used on any flight to reduce the contingency fuel to 3% of total trip fuel rather than 5% thus allowing a little less fuel to be loaded and saving (a small amount) on the burn as well as perhaps allowing a larger payload. Copied from our manual: "The en-route alternate should be located within a circle having a radius equal to 20% of the total flight plan distance, the centre of which lies on the planned route at a distance from the destination of 25% of the total flight plan distance, or at least 20% of the total flight plan distance plus 50 nm, whichever is greater, all distances are to be calculated in still air conditions." Fortunately it's easier in practice as the company have worked them out for all the routes that can benefit. It's up to the skipper on the day as to whether they want to use it or not.
There is also the option to reduce to minimum contingency (250kg on a 321) in which case the en-route alternate must be within 150nm of track and be at least 30 minutes flying time from the destination but obviously you need it fairly close to destination as you don't want 5% of the remaining trip fuel to be more than 250kg. This option can only be used if you unable to load the normal 5% (or 3% if are using that procedure) due to a performance or payload restriction.
In both cases the airfield must be above the planning minima for +/- 1 hour of ETA.