It appears that many startups are using both licenses to create commercial FOSS products (note I am here more interested in complete products not libraries). Is the 3-clause BSD more protective for the startup rights than AGPL without creating the stigma that's around GPL? Does it make other for-profit companies and competitors think twice before repackaging, rebranding and selling the FOSS software as is for profit and simply making easy profits off the back of the original FOSS author?
Is the 3-clause BSD more protective for the startup rights than AGPL without creating the stigma that's around GPL?
Hard question to answer, because I don't accept that there's a "stigma" around the GPL, and variants. Some organisations definitely don't like copyleft-licensed code; for them, see below. Many other organisations are just fine with it. Enough people are suspicious about the pervasiveness of the idea that there's something wrong with copyleft that experts give talks like Who wants you to think nobody uses the AGPL, and why.
But be clear: if by "startup rights" you mean "preventing repackaging, rebranding, and selling the FOSS software as-is for profit", then 3-clause BSD, and all the other weak free licences, do next to nothing to protect those "rights".
Does it make other for-profit companies and competitors think twice before repackaging, rebranding and selling the FOSS software as is for profit and simply making easy profits off the back of the original FOSS author?
I'm not aware of any academic work on this, though I'd like to be enlightened. But in my experience, the organisations that are most worried about the GPL and other copyleft licences, who won't let code covered by it anywhere near their development processes, and who often won't let it through the door at all, are exactly the ones that want the right to resell someone else's work under their own brand, and with no more acknowledgement than the couple of paragraphs the weak free licences require, often buried at the back of a manual or deep-down in some menu.
The way I see it is that the weak free licences are primarily about making software free. People who choose them don't really care if their code stays free, as long as it gets used. That is a perfectly legitimate choice for them to make, but if you decide to make it, don't be surprised when your work is commoditised. You told the world you were happy with that in your choice of licence.
The copyleft licences are about keeping software free. People who choose them would like their code to be used, but aren't willing for that to happen if the users aren't going to keep it free.
Work out what's more important to you, and pick your licence accordingly. Do not indulge any faint hope that, by picking a weak free licence, the world will keep free what it builds on your work, out of some sort of perceived debt of honour.
There is a world of difference between GPL and AGPL.
My experience with AGPL is that any corporate lawyer who looks at it first faints, and then demands company-wide banning of touching any AGPL software with a 10 meter pole.
GPL will get you users, and lawyers rarely care.
AGPL will get your software banned under penalty of getting fired.
For example you won't get any users or contributors who are Google employees.