I understand that the boundary you mentioned held significance within Junior football but does not apply within the pyramid, I believe that the clubs thinking of applying to the pyramid meet the criteria for both EoS & WoS. It's been years since the West Lothian sides played against teams that would have been considered some of our 'traditional rivals', clubs adapt and find ways of making their situation work for them.
Personally I don't believe that teams from West Lothian playing in different leagues would cause any 'real world' issues.
You are right that these considerations (amongst many others) will need to be taken into account by clubs when make their decision, I truly hope that they are and each club makes a decision it is the right one for them (personally I don't know what clubs intend applying to what league but believe they should be allowed to apply to the league that best matches their vision for the club).