About your alien invasion example, I think you might be a bit exaggerating the difference between 5e and 4e. Antimagic fields and other fictional elements that cause penalties or prevent actions could exists in either. I have to note that the element that caused disadvantage to basically all rolls seemed to be designed to punish non-caster (or it does, whether the GM intended that or not) as many spell effects just work without a roll and thus are unaffected. Not sure how relevant that is for agency, except that it might have caused some frustration in the players as their sensible-seeming attempts kept failing due this effect.
My main observation was how you described 5e method of assigning DCs and such as 'arbitrary' compared to clear level appropriate guidelines of 4e. It is funny, because I would describe them as completely opposite manner. In 5e the DC actually represent something concrete, they're reflection of the fictional reality, whereas in 4e they're just arbitrary and do not represent anything concrete beyond being sufficiently challenging to the players (I think they tried to walk back that in some of the later material.)
Now, considering that you were running a scenario written by someone else, containing a lot of atypical elements, I can understand how it might feel 'arbitrary' in that context. What is the proper DC (or even skill) for operating alien hoverboard in D&D? Who the hell knows, there normally even aren't alien hoverboard in D&D! But with a GM who has a good mental picture of the setting, consistent(ish) approach for assigning DCs and players who are familiar with this it is not arbitrary. The same task will have the same DC regardless of the level of the character attempting it.
As for the second quote, I am not quite sure what your point was there. If it was to point out that in 5e there are many differnt way in which the GM could apply force if they so chose, then that is not in dispute.