The adventure is written for up to five PCs not six, it on page 2 first sentence of Running the Adventure. If you run it with six or more then their advice and setup indeed doesn't make sense and the PCs will handily win most encounters.
I have run Philanderer three times, each time the initial goblin ambush was challenge for the PC. Two reasons their high stealth resulted in a surprise round each time and they are armed with shortbows.
This blog post,
a near party kill, is typical of how the first encounter goes for me.
As for in-game motivation, the adventure has the party driving a wagon full of supplies to Phandelver. Out of a five person party may be one or two will looked like a heavily armed warrior. The rest will be dressed in more ordinary clothes little different than what commoner wear. The party in my blog post only Vognur looked like a armed warrior. Sidwin had some gear and looked like he could handle himself in a fight. But Squirrel was dressed in ordinary clothes and Ara was dressed in robes that marked him as slightly more wealthy.
The goblins also have a wisdom of 8 which implies they would tend to take more chances than a more sensible group would. Combined with the overconfidence resulting from their use of missile weapons and stealth ability to me makes an ambush of a 4 to 5 person party involved escorting a supply wagon makes it a plausible encounter.
Is the setup and advice perfect? No but I still give a solid A as far as these goes. However also from experience running 5e, if you have less than four or more than five, then the encounter will likely go very different when run multiple times. I don't think the writer of the adventure realized how crucial that is.
Especially in hindsight when 5e first came out a lot of people wanted to try it. This often resulted in oversized parties. So if I were to write a intro adventure like Phandelver for the next hot edition, I would spend some paragraph on how to scale encounters up (or down) to account for the size of the party. I am not a fan of scaling but the point of Phandelver is an aide to the novice referee. They need to know what the effect of having a 8 person party swamp everything or what happens if there are only two players involved.