小中大instrument is serving as a "reference" only meaning its never the REAL etch-rate on YOUR SAMPLE. However, its still serving as a very important reference for knowing some thickness information because otherwise you have no idea at all how the thickness relationship to be on your sample. The value you see in your software should be calibrated by the service-engineer and as you said by using Ta2O5 as standard. Ta2O5 (or some use SiO2) are typical samples using for sputtering rate check on surface analysis instruments.
And further to your question because sputtering rate is on Ta2O5 and you do not know what is actual rate on YOUR SAMPLE. In this case, what exactly is your sample material? Sometimes it may be possible to get some reference on the internet about different materials sputtering rate as reference to SiO2 or Ta2O5. So give it a search on Google or Baidu for it. On the other hand, certainly it is impossible to know sputtering rate on ALL materials in the world. So in this case, a very typical way when explaining a depth profile data, one would put into the data stating "sputtering rate is xx nm/min on Ta2O5/SiO2 standard sample". It is widely accepted by the surface analysis field.
Answer 2: Usually no need to consider the angles how photo-e comes out because basically they're coming out at ALL angles. Usually what would affect your data are:
(1) Angle between X-ray and Analyzer
(2) Angle between Analyzer and your sample-flat-surface.
For (1) it is instrumentation so you don't care much.
For (2), it may relate to later part of your question. As continue to guess your system is Thermo 250 or 250xi, YES the analyzer is perpendicular to the sample. Its called as Take-of-angle (TOA) 90-degree. At this angle, the sensitivity would be highest (just imagine because sample is directly facing to analyzer) while the detection depth is deeper. If one tilt the sample stage so making the TOA is smaller like 90 > 45 > 30..., then sensitivity will get lower