I'm a little confused where your friction with the system is, if you could elaborate some more? I can keep manually exploring when the auto-explores are maxed out with or without claiming them first... and I can still manually explore while it's auto-exploring, it will just pause the auto-explore progress until the main explore bar is filled again after I've left campaign. I can also manually explore in the area where it's auto exploring without any problems?
Are you experiencing a bug with the campaign where it won't let you explore the area you're auto-exploring, or am I just not quite getting what the issue is? Do you not like that it pauses auto-exploring while you're manually exploring? If it's the latter, the design philosophy goes that it's not there just for you to get free extra bonus turns indefinitely, it's there to disincentivize botting while you aren't playing the game by tossing you something for going away.
I don't think it quite lives up to its intention in that regard, but there isn't a lot they could do about that except make it spit out a new currency instead of pebbles. I wouldn't be against that idea, both to slow down the ever-increasing speeds at which the game seems determined to print them out while there's literally nothing worth spending them on, and because it would itself not be a bottable currency if only implemented there.
Overall though, sorry, but anti-botting measures are worthwhile, so I wouldn't support its total removal. Certainly I think it can be improved upon though!