As
@Domh245 notes, the handrail "issue" has only arisen because of some specific DfT requirements relating to crush-load capacity in the South Western franchise requirements. Effectively Siemens gambled on the Thameslink spec being pretty close to the "ideal standard" for high-capacity metro trains in Britain for many years to come and were caught out when the DfT moved the goalposts around a bit and started to require ceiling-fixed grabrails in the exact places that Siemens had chosen to put wiring harnesses and other bits of electrical kit. It's not a defect or anything like that, just a small limitation on flexibility when it comes to the saloon layout.
The toilet thing isn't an "issue" at all - the Desiro City design is perfectly capable of accepting toilets, as the 700s show. It's very simply the case that SWT decided that they didn't need them in the 707s, and SE have now decided that they can't be bothered paying to retrofit them. There is absolutely nothing stopping Siemens from tendering a Desiro City design that's absolutely bristling with them should that be what SE want.