From the playthroughs I've see on youtube, they've said you can play it with out any of the extras. It just makes the game easier, which I'd think the strategy guide is going to lead players more towards doing.
It looks like the change in difficulty makes the difference between the game being playable and the game being exceptionally difficult (beyond the difficulty settings on the main menu). There are multiple examples of the strategy guide telling players to "go back to _____ level and ________ in order to be able to play through this level".
This was annoying enough in X3, where there is no clean way to go through the first 8 levels. And, X3 is relatively simple compared "Mega Man 11".
The Mega Man Legacy Collection is split into two parts, 1-6 and 7-10 and the X collection is split between 1-4, 5-8. Not sure what exploits you're referring to, but to my understanding, they still work.
The first game had an exploit where the player could pause the game (using "select" on an old Nintendo controller) while fighting most of the bosses. Pausing the game as the shot was hitting or passing through the boss, then waiting a few seconds, would allow the shot to damage the boss multiple times, every time the game was paused and resumed. (In theory, a player could kill the Rock Monster with one pellet shot. But, a stronger weapon would still be better.) According to my friend, the pause trick did not work in the legacy collection. (But, he did manage to beat the game, including that awful boss rush at the end.)
"Mega Man 3" had several exploits involving the second controller. Holding the right buttons (or combination of buttons) on the second controller would effect how high a player could jump or the speed of enemies. These exploits would carry side effects. But, they were still pretty useful.
I could never beat "Mega Man" without using the pause trick at least a few times. (Elec Man, the Rock Monster and the final boss rush were consistently challenging for me.) With "Mega Man 3", I generally did not use the exploits, but was not above doing so occasionally.