Yes, Westminster has decided that ORR as the regulator gets to decide Network Rail's budget. But if Transport Scotland were to chuck extra money at NR to do stuff, do you think ORR will say "No you dont unless DfT agrees to it"? If NR Scotland were fully hived off, would there not need to be some kind of independent regulator? Are you suggesting a separate ORR for Scotland?
Also, the regulators powers are quite wide ranging, and although they have been given to them by Westminster, they are not dictated to by Westminster - ORR has the power to instigate a periodic review (I believe Tom Winsor threatened the Labour Government with one of these once), and should the Government attempt to overrule the independent regulator, theres no doubt it would lead to a judicial review in the courts, plus the associated impact on other regulators, such as OfCom, OfWat and OfGem - and I'd expect the utilities in those sectors to be up in arms about Government interference in independent regulation.
So really, ultimately, the idea that the Scottish Government has "no powers" over Network Rail is risible. They can - and do - decide what they want Network Rail to do, and they give them the funds to do so. If they wanted the Highland Main line dualled and electrified to Inverness, theres nothing stopping them from chucking £3billion at Network Rail and telling them to get on with it. What powers do YOU think they need? And from whom?