रामरामराम।
श्रीगुरुभ्योनमः। हरिःॐ।
The noun-bases of ततः, इतः, अतः are ततस्, इतस्, अतस्। whereas for पुनः, प्रातः etc are पुनर् , प्रातर् , etc. Hence there is no रेफादेशः for पुनर् प्रातर् etc.
The Sutras set for processing रेफान्त words are totally different from the Sutra sets of that of the words ending with सकारः। So,
पुनर् अत्र - No Sandhi and it is पुनरत्र।...
But in पुनःपुनः the rephantha of first word gets visargadesha thence since succeeding letter is पकार gets उपध्मानीयादेशः or विसर्गः optionally.
After initial instructional knowledge of Sandhikaryas, when one approaches Paniniyam by Sutra-based (Ashtadhyayi based) process of Sandhi karyas these subtle differences can be known.
Paniniya Sutra based (Ashtadhyayi based) knowledge can be gained by perusing Laghu / Vaiyakarana Siddhanta kaumudee or Kashka.
जयतु संस्कृतम्।
पुरुषोत्तमशर्मा।