Let me explain what I mean when what Flowey did in Undertale Yellow doesn't make any sense in a long and thorough explanation.

When Flowey found out about Clover for the first time, he refrained from killing them and absorbing their soul for no reason and instead chose to watch their small adventure that inevitably ended with them staying with Toriel many times. This is out of character for UT Flowey as he tried to kill Frisk when he found out about them, only failing due to Toriel's interference and Frisk being more determined than him. Another good reason for Flowey to kill Frisk is that if he was successful in killing them and absorbing their soul, he would have a clear way out of the underground by killing Toriel and absorbing her soul then use the hole where humans fall into as an exit out of the underground. This solution would not only skip the complicated process of figuring out the location of Asgore's human souls but replace it with a far simpler way in the form of killing six humans and absorbing their souls to become god in the Surface.

There is no reason for Flowey not to kill Clover in UTY with such an obvious solution available to him and unlike Frisk, Clover is not more determined than Flowey, giving him countless attempts to separate them from Toriel. Flowey would inevitably succeed in separating Clover from Toriel, killing Clover and absorbing their soul, leading to the Meta Flowey Boss Fight on the first run.

Obviously, Flowey stated that he and Clover would be stuck at stalemate forever in UTY's neutral route, so he would eventually give up on defeating Clover with one difference being that he'd skip the Meta Flowey Boss Fight at all times after seeing that it didn't work out, which is in character for Flowey; he won't bother to waste his time with something that failed once. He skipped Photoshop Flowey Boss Fight after seeing that it didn't work out when you do the neutral route for the second time in UT. He would do the same with Meta Flowey Boss Fight, preventing the possibility of it happening hundreds of runs later.

With that in mind, another good option for Flowey is if he delivered Clover's soul to Undyne's home and then watched her deliver it to Asgore. After that, Asgore's actions of summoning seven jars containing five human souls to put Clover's soul in one of them would not only give Flowey clues about the human souls' location but create an opening that he would exploit by following where six human souls went underground.

By doing that, Flowey would inevitably discover the location of six human souls due to countless retries, which means that one of his attempts will eventually become successful. After he figured out the location of six human souls and absorbed them, he would mock Asgore and torture him to his death. He would then exit the Underground to kill one more human and absorb their soul to become god.

This solution is most unlikely to fail, and it is even more unlikely for Flowey not to consider it if we decided to entertain the possibility of Flowey not going with it. The chances are that Flowey would definitely become the god that rules the Surface as his playground before Undertale Yellow events would even begin, let alone Undertale events.

Still, if the one in a million chance where this solution somehow failed happened. The events will only continue as normal until the moment when Clover stepped outside the Ruins and died a lot due to a skill issue.

At that point, UT Flowey would handle Clover's situation a lot more professionally than the mischaracterized and dumb version of him did in UTY; UT Flowey wouldn't bother to reset as doing so would only jeopardize all of Clover's efforts and, by extension, his efforts, erase any progress they made. He would only reset as a last resort.

And at the same time, UT Flowey would also be a lot more focused on making sure that Clover made it to Asgore on the main path. This means that UT Flowey will go with any means to complete that goal like giving Clover helpful pieces of advice about monsters they're fighting or puzzles they're solving and giving them directions as to where they would get/buy healing items or stronger equipment, manipulating Clover into thinking that killing monsters is okay and keep killing more monsters, making them grow a lot stronger over time. Flowey would easily give Clover healing items or stronger equipment if the situation demands it; I think that Flowey would definitely give Clover Worn Dagger, Delta Rune Patch and Heart Locket to increase their fighting chance greatly since Clover will get 15 ATK from Worn Dagger and 25 DEF from Heart Locket and Delta Rune Patch.

And there's no need for Flowey to consider the alternate path option in the worst-case scenario where Clover can't solve any problem on their own. Any problem that Clover struggled most with could easily be solved by Flowey. Let's say that no matter what they do, they always hit dead end with unavoidable lasers coming from laser drones for example. Flowey would easily disable them, and what'll happen if Clover struggles too much against a certain monster? Flowey easily killed that monster in secret. Anything that Clover can't do, UT Flowey can do for them.

There are still other options to consider. In fact, Flowey could clear out the whole underground and solve every puzzle, leaving only Asgore, which means that Clover won't encounter any obstacle or enemy, and there are no variables to consider, so Flowey won't come across issues like Clover staying with Martlet for example. And that's without mentioning shortcuts shown in UT.

Flowey could easily convince River Person to come to Snowdin and convince Clover to take the ride to Hotland, remove restrictions that Alphys imposed on the elevators and convince Clover to take the ride to UG Apartments. Free up UG Apartments' elevator and convince them to take the elevator to New Home, which leads them to take another elevator. By that point, it's just a walk to Asgore.

There are many ways for Flowey to make sure that Clover reached Asgore on the main path, which eliminated the need for alternate paths.