I believe the later one (2.) is more reasonable, I guess the rule is set only to prevent the president wasting company's asset. Am I right?
That is the spirit of the rule. You cannot skip adjacent available cities. If have city A and it is connected to B and then to C (A - B - C), you cannot skip over B to build in C unless B is filled up (for the Step you're in).
In s standard game, there may be positional reasons why you might want to skip B and build in C, but the board of directors won't be convinced of this use of company funds.
But what if there is another city, D, that is several occupied hops away? Can you build in D if B is available? I think the answer is yes, regardless of the cost of D relative to B.