Your example is the absolute best case scenario, so yes there charge the same or more. Fine
1) You say the choice is not based on price, why? Because it's B2B? I've sold B2B for 12 years and maybe a handful of times would I say that the customer did not consider price a factor in any way. That is extremely rare, and a fallacy in bootstrapper circles.
First off, most B2B you will sell is small/mid size and price is 100% a factor there. 99.99% of your enterprise sales will be to departments inside a larger enterprise, not a full scale enterprise solution. For departments in enterprises, price is 100% a factor. (anecdote, have a $10 Billion dollar private co that uses HelpSpot for a pretty important product that doesn't renew support bc of cost).
So you're left with the true enterprise solution sale which is insanely rare at the one man shop level. Rare is generous, it's really unheard of.
2) Price messaging is important but hardly the holy grail. In any sale you're trying to stack up enough wins vs the competition for you to get the sale. So you might lose a few points with some customers for being cheaper, but you'll also certainly win a few points with others.
You've also totally disregarded brand strength. Most bootstrapped startups have 0 in the wider B2B world. Very often you'll be up against funded or public competitors with some to very strong brand recognition.
It's a fallacy that just being higher priced means people think you're better. Customers aren't stupid. A strong brand positioned as premium can demand a higher price. Very few people reading my advice have anything close to a strong brand.
Honda sells the Acura MDX for $50k and the Honda Pilot for $30k even though they're basically the same car. Sure there are some enhancements for the MDX but not $20k worth. It's because the Acura brand is premium. You don't have a premium brand, nor are you ready to start out day one (or probably year one) defined as a premium brand. They'll be way too many holes in your game to pull that off.
The Honda Pilot isn't "cheap crap", but it's also not pretending to be something it isn't. An even better comparison is say the Kia Sorrento. Kia knows it can't directly match the MDX so it works from a different angle.
3) Saying "offer the same price" is very easy here but less easy in real life. It means having the exact same pricing model and tiers. Right there most direct comparisons start to break down. What's in my "pro" plan isn't the same as what's in your "Team" plan, etc. I'm per user, you're tiered, I offer free setup, you charge a setup fee, etc etc etc.
So when the prices seem similar and the features seem similar and they have more brand strength you're going to lose those battles a lot.
4) You make the assumption there will be feature parity. That is incredibly unlikely. Your year one bootstrapped startup will not have feature parity with a 5 year old established app. There are other angles you can play like having a workflow that works better for certain kinds of companies, but feature parity will not (and probably should not) be one.
5) Freemium and charge less are not orthogonal at all. Freemium is simply your advertising budget. You can't actually buy Google ads because you have no money. Most SaaSs are so cheap to run now though that you can afford to give away the service itself at some level.
Once they're using it, in fact, you probably can charge a bit more since they're committed (in theory), but in any case still undercutting the competition is likely to your advantage as ultimately the customer is still going through the checksheet of factors for buy/don't buy. If you do charge more it will have little/nothing to do with having to charge more for freeloaders, but rather because you'll be able to charge more since the customer is already committed to your product and moving would be a hassle so paying you a bit more for those extra features and not having to move is a convenience fee.
This is certainly based on the idea that you've built your freemium app in a bootstrapper friendly way. If you go full VC startup and build an app that's expensive to run this all breaks down. But I'm not speaking to those people.