Yes. There's really two questions here:- The procedures of the Railway Operators and the Law.
The vast majority of rail journeys in Scotland are provided by First ScotRail and these are a) subject to Scottish Law, b) subject to that Company's policies and custom which tends not to pursue Criminal Prosecutions as their English and Welsh counterparts might do. They might consider a breach of Contract and would bring such a Prosecution forward to the Sheriffs or Justices or seek the intervention of the Police to take forward a Criminal prosecution to the Procurator Fiscal. However, some journeys are undertaken on other UK operators (e.g. East Coast, Virgin, Cross Country, etc.) and these Companies will be inclined to investigate and process irregularities much as they would in England; their Contracts (with a small number of exceptions) will be subject to English Law.
In terms of process, FSR are less likely to pursue a claim in the Scottish Courts as a private prosecutor (as their English counterparts do), and so the quantum of any claim and therefore the penalties that you asked about are likely to be very different - e.g. the costs and Fines of a Criminal tariff in England & Wales as opposed to the costs and losses of a Civil action in Scotland.
You have specifically asked about Fare Dodging, and as you probably know, serious Offences are considered fraudulent. The Fraud Act does not apply in Scotland, although such offences in Scotland will be treated under the Common Law model of Fraud.
The Scottish Executive is under some pressure to introduce more effective and comprehensive Fraud legislation.
[My knowledge and experience of Railway offences in Scotland is slight. Perhaps someone else will point out any errors or omissions.]