Substantial changes to manuscript in the revision process Is this acceptable to revise a manuscript more than what reviewers suggested? In fact, due to some issue, the authors may find out that there are some issues even reviewers could not address, so they decided to extend the revision border.

P.s. What about imposing changes so that affect the title, abstract and a large portion of  manuscript. In an advise to a friend of mine, I warned him of doing so because it results in a new paper not a standard revised version. Nonetheless, I told him that is the case of such comprehensive revision he should carefully explain reasons behind that decision. Can such rational explanation convince the reviewers to consider another round of review?
You appear to be asking about making substantial unrequested changes to a manuscript after review. If it's because you have realised that the paper can be improved, without making it a totally different paper, then this may be a reasonable thing to do - but ultimately the judge must be the journal's editor. 

What is vitally important is that you talk with the editor about it, and are clear about the scope of the changes. It sounds as though the changes are big enough that, if made after review, they should probably trigger another review. The editor may agree with you that the changes are worth doing and that it is worth waiting for another review - or they may not be prepared to do this, in which case you will have to decide whether to leave it as-is or to withdraw and start the process again. 
Either way, it's likely to involve a substantial delay in publication of your manuscript.