It doesn't make software patents legal - and in fact, software patenting is explicitly not allowed in Europe already, and this doesn't change anything about it
Formally, it doesn't. In practice, just as the European Patent Office creatively reinterpreted the European Patent Convention (EPC) over the years and as the US C.A.F.C. kept broadening software patentability (until the Supreme Court reigned it in a bit again — and yes, I know they started it in the first place), it is unlikely that a an incrowd of patent people will forever be very stringent regarding interpreting the boundaries of patentability (hammers, nails and all that).
And since the Unified Patent Court would be the highest authority regarding the interpretation of the EPC (the EPC is not EU law and hence would not be subject to appeals at the European Court of Justice), there would not be a body of people outside the patent system to overrule them. There is no need to look for conspiracies or bad faith in this. It's just that if you have a lot of deeply specialised people together that basically decide themselves about the rules governing their own domain, you get bad rules due to the narrow field of vision (no matter how openminded the people involved may be). Getting the EPC renogotiated would be even harder, and given that the people involved are mainly the specialists from national patent offices, it's mostly decided by the same incrowd anyway.