The roles are just suggested right? Not set in stone per say?
I feel like we are missing some concern you have here. Why are you asking?
No, we have no ninjas to send to your house if you insist on using the Atlas AS7-D as a Sniper instead of a Juggernaut. We wouldn't send them even if we had them.
Can you put four Atlas AS7-D in a Fire Lance and say you are following the Alpha Strike Companion Force Building rules? No. The AS7-D is a Juggernaut and you need at least 3 of the 4 members in the Lance to be Snipers and/or Missile Boats. You can have one Atlas AS7-D in a Fire Lance, you have one freebie (only 3 of the 4 have to be Snipers and/or Missile Boats, the last one has no restrictions at all).
Are you required to use Alpha Strike Force Building rules? It's your game, it's up to you. Unless it's somebody else's game, then it's up to them. Again, no ninjas.
So then the unit card on the MUL takes precedence over the AS Companion book?
Not sure what your question is here. The AS Companion does not assign unit roles to individual units. Even p134 "unit role classification" says "This classification can be extremely subjective," and "Keep in mind that, ultimately, the unit’s stats do not always
define its role, so much as how the unit is intended to be used. The role definitions provided in this chapter are merely a guide for players working from raw stats..".
The stats for the RFL-3N do not say Sniper. The fluff of the BattleTech universe has always described it as a Fire Support 'mech. So regardless of any stats, rules, number crunching, we assigned it to Sniper (it's definitely not a Missile Boat). Would another twin AC-5, twin large laser 'mech also be assigned to Sniper? (It's armor certainly helps "doom" it to Sniper.) That's what we mean by the role be "extremely subjective". The p134 section is to help guide a player for where there is no history/MUL assignment already done. But even those are not "rules", they are guides. There is no wrong answer, except you can only assign one. :)