Read Between the Lines
Let me translate this for you:
Not having much experience my hiring manager offered me another job
that is tangentially related to the job I love. And if I perform well
on that semi related job for six months I could be considered for
senior level position that I would love to do.
The hiring manager is saying, "You are not qualified for the senior position. If you would like another open position we have, we are more than happy to hire you." That is what he is promising.
On the future with the company, all he is saying is "you can re-apply for the senior position in six months". You admit yourself you don't have much experience. The chances of that senior position really being open in six months if it's an upcoming start-up are low. The chances that you will go from "not having much experience" to being prepared to take on that senior role are likely low.
But it isn't impossible!
Of course it is a non-zero chance that it could happen. You could be a born natural for the company and the role. And that senior level position could sit there open for the next 6 months as the entire company realizes your inherent merit.
Much more likely is that you will be put in the junior level position, and remain there, with promotions in line with the position you were hired for rather than the position you applied for.
Regardless, you're not going to get a promise from the hiring manager. Want to test the waters? Ask him if you can speak to the other senior-level management and get their word that they'll hold the position open for you for the next 6 months.
Warning: this has a high probability of having the hiring manager revoke the offer for the junior level position. He/she may very well expect you to read between the lines, and pushing too hard at the start may leave a poor taste in his/her mouth (as well as indicating that you are only interested in the senior level position you admit you aren't qualified for rather than the company and gaining experience which is what the company would expect).
Each According to their ability...
What it comes down to is whether or not you'd be okay with just working at the junior role for the next 6 months and working your way up the ladder. If you like the company, isn't that more important than your job title? Is the title more important than the experience and potential for growth you'd get from the new job anyway?
To get a similar senior-level job in the future, will this be a stepping stone (regardless of if you get it in this company or not), or will it be better for you to stay in the current job? That's how I think you should make your decision.