Minor modifications shouldn't require a new full review cycle, maybe just the editor takes a look, or just some quick check with reviewer to see if they accept the change.
Rejecting pending resubmission is for larger changes which require a more thorough review, but the journal is still interested in publishing the paper. This might be a section that requires more explanation, for example more details on how samples were controlled for other factors.
Also as mentioned a full rejection doesn't automatically mean the paper is rubbish, it could just be the journal doesn't consider it a good fit or similar. It's not uncommon for a paper to go through multiple rejections before getting published.
At least that's my understanding based on a close friend who publishes papers, feel free to correct me.