Once Containment bugs, can College of Winterhold questline be completed

Don't know if it's necessary to put this here, but: spoilers ahead!

So I've run into the bug on the Containment quest, whereby it doesn't trigger after the completion of Revealing the Unseen quest. After the explosion caused by Ancano, I was asked to find the Arch-Mage, but the Containment quest never came up. I found his body in the courtyard, but everyone in the college is just going about their business as if nothing happened…

After spending a great deal of time looking around the web, there seem to be 2 likely causes of this:

• A dragon is in the area (this was the case, because as soon as I left the college, it swooped down)
• There were uncompleted side quests for other college members (this was also the case – I had 2 that I had not completed)

I also found a command to start the quest after Containment (I had played a good 6+ hours before this happened & all the autosaves got overwritten as I was running around trying to figure out who I should speak to, so can't load up an old one). I did try starting Containment (Quest ID: MG05), but since this ID is before Revealing the Unseen (Quest ID: MG06) this does not appear to work. The following commands will skip Containment & start the next quest:

setstage MG07 0
player.additem 000a34f8 1
player.additem 000f1b33 1

My question is, has anyone had this issue & used the above commands to continue the quest line? By using this command, will the quest chain just carry on as normal, or am I going to run into something else further down the line? If I do, I'd rather not waste the time…