1. Bonus Stat points are functionally just the same as stat points you're acquiring from your gear. They don't affect the growth pattern or anything so there's nothing to really think about. You gain them upon level up and further down the line, once you get to Master Levels, you'll have the option to buy more. For example, if you have +10 AGI from a glove and have 10 points in AGI from Bonus stats, it's just 20 AGI total. It would be the same as if you had glove that gave +20 AGI.
2. Not necessarily. The reason for getting INT is for the passive skill "Battle Tactics". The skill gives a ridiculous amount of extra Critical Damage and the condition (investing in INT) is extremely easy to reach once you get higher levels. The benefit caps out at 1000 INT which is why some might tell you to invest in INT if you haven't reached that yet. However, do note that once you get to higher levels, your accessories, cards, titles, and honings will provide a fair chunk of INT. Until you reach that cap, it is true that mathematically getting INT is more damage than using STR, especially considering how little impact STR has in RO2's damage formula. If you don't want to worry about until later down the line, the other recommended stat is VIT.
3. Dungeons have nobody queueing for them so don't worry about missing them. You can skip them and come back to them when you're overleveled because they don't offer good gears anyways. They don't even offer the original feel of the achievement because a few years ago the formulas were altered and ruined the content, making everything drastically easier.