Saved by NPC encounters. Yay or nay? How to handle

Future first time dm here. I'm setting up a homebrew campaign for a group of friends for a game that will start later this year. I've noticed in my planned encounters I have a recurring trend. Putting the party in encounters that they are not able to win unless they run, and having them be saved by an npc important to the story.

The first one I have planned introduces one of the big bads of the whole campaign. The party will do something that makes him mad very early on. He finds them shortly after to seek revenge. This is to have take seriously the big bad's faction who at this point will have only been portrayed as bumbling thugs. Its also to show the party that in certain areas, a specific type of magic is highly frowned upon by this faction so they will need to be careful to avoid their attention.

The other one comes much later in the campaign. More of an important side quest. The party takes on a chain of quests to eliminate shadows holed up in caves on a mountain. They realize too late that they are led by much bigger intelligent shadows and there are tons of them. A messenger of this world's god of light, the main god, shows up to aid them, mostly helping their escape. He explains that their deeds so far have impressed the god but they will have to come back later when they are stronger as even he is not enough help to achieve this now.

How do you guys feel about this kind of thing? I don't want the players to feel like they're in a no win encounter. But I still feel like for some specific story beats, this can work. Like they won't be useless in these encounters, they can hurt the enemy, definitely take out the lesser enemies. 

Do you guys think I should avoid this kind of thing? If so how then would you advise me to go about this?

First question, how far are you planning ahead? Chances are, a lot of the encounters you're planning won't even be used if you set things up for more than a few session away. Lay the groundwork of your plans, but don't get attached. The game is incredibly expansive and adaptive, and making a railroad-type experience only increases the chances of deviation. I suggest letting the players lead the way for a more natural experience.

Probably fine only to do it once, and even then, let there be multiple ways out. The second time, players will start to feel disgruntled and that they have no control. I've had first-time players drop out of games very quickly because they didn't experience the degrees of variety that I drew them in with in the first few sessions, because they were the first few sessions. Many of the same story tricks don't work well more than a few times. Instead, leave questions on the table that the players have to seek answers to, to help them feel proactive.

The first one I described with the faction leader will happen in either session 2 or 3 I imagine. It will be unavoidable unless the party decides to not help an innocent family getting killed by other members in this faction in session 1. Possible, but doubt it. The faction leader does give them the option to join his faction to make up for the killed members. Or they can be taken to jail where this faction, which is very anti magic, has ways to strip them of their magic powers. I'll never actually take away their magic but I would have a way to temporarily nullify it just for a session or two. But basically they will most likely want to fight.

Other than this, I'm not 100% sure about the second encounter I described. I might be able to work that in another way. Like perhaps an escape encounter which will lead them to the God's messenger I described. Not sure just yet.

I appreciate the advice. I do plan a lot in advance for main story beats. But I also plan for at least one, sometimes two other possible choices or paths for each one. So I freaking hope I'm doing good lol.

I'd advise against any situation of forcing the players into a combat they cannot win. It is fine for there to be combats they cannot win in the game, but it should always be their choice to take those on or not. If the dungeon full of shadows is too hard for them, why send them there? If they choose to explore it at a too low level that's fine, but I would not send them there as the only thing they can do to progress the story.

Having NPCs available to help the players is fine, but similar to the above there should be some degree of choice in the matter rather than it just being something that happens. For instance with the Cleric of Light - he might be locked in a room or caught in a trap and if they free him he will advise them to leave / help them. For the gang, having an NPC guard currently investigating the gang join them in the fight is fine as long as that NPC doesn't have plot armour and can die if they don't work together with him.