This is a rather complex question as there are multiple variables and many proposed designs for thorium fuel cycles to consider as well; but it seems your primary interest is in whether or not leaving the Pa-233 in solution will adversely affect the thorium nuclear cycle to the point where it makes more sense to remove this isotope to be reintroduced after it beta decays to our much needed U-233 fuel.
To answer this question briefly let's first assume a thermal reactor (as in the neutrons are well moderated and have energies ideal for fission of U-233). Next let's make an assumption about composition with 98% Th-232, 1% Pa-233 and 1% U-233.
The cross sections of each of these isotopes (how 'big' they are to a thermal neutron) are approximately: Th-232, 7.37 barns for absorption; Pa-233, 40 barns for absorption; U-233, 529 barns for fission. If you do not know what a 'barn' is, basically it is nothing more than describing the 2D size of the target nuclei as far as having an interaction with the incoming neutron. 1 barn = 10-24 cm2 and was named such because on atomic scales, as the old saying goes, "...is as big as a barn."
This information can be used to derive the average distance a neutron will travel before it has a 'collision/interaction' with one of these atoms (also
known as the transport mean free path). The function is as follows:
$$l=\frac{1}{\sigma N-\frac{2}{3A}}$$
Where:
Since they are all very similar in number of protons and neutrons we can eliminate the $\frac{2}{3A}$ term. Also, this function is primarily used for scattering and calculating energy loss of a neutron through a given depth of material but it works just as well for absorption leaving us with:
$$l \sim \frac{1}{\sigma N}$$
This formula gives the average (ish) distance a neutron will travel through a material before having an interaction with an atom (absorption, fission, scattering, etc.).
With some quick number crunching (skipping the exact number densities and going with the % of compositions) we can easily see the average distance traveled by the neutron is over an order of magnitude shorter for the U-233 and Th-232 vs. the Pa-233 isotope so its effects on the 'efficiency' of this reactor would be negligible.
To answer your questions:
- Does Pa-233 formation affect the reactor efficiency? Yes.
- Is it critical to remove Pa-233 to have a viable thorium fuel cycle? No.
- Does the geometry of the reactor effect efficiency? Yes, but that is a whole other question. ;)
Hope this helps!