The line by its very nature has an influence on all leagues, directly or indirectly. Ignore it and we open up the scenario of Forfar West End in the LL, and Forfar Athletic in the HL. So the EoS cannot escape the fact that the demarcation line exists and they have to be mindful of its potential impact further up the tree, they know this. Would the LL accept an EoS Champion from north of the line for example?
That's a different issue from clubs applying, as you say anyone can apply for any league (as West Lothian/WoS demonstrated), it doesn't mean to say they will be accepted.
There has been a desire from some within the EoS to set a northern boundary to match the HL/LL line, this issue will probably settle it once and for all.
As for travel, that almost certainly will colour some clubs attitudes, understandably. As will the upheaval of trying to accomodate Tayside into the sturucture.