In any case, canonical Pali also uses dissimilar conjunct consonants (so if early Brāhmī didnt use dissimilar conjuncts, it couldn’t have been used to write Pali accurately either) - for example I found these in a random search of the Pali canon, I am sure there are many more examples.
- tra & sta in tatra, utrastamidaṃ, anutrastaṃ & nāññatra
- tri & dri in nāññatrindriyasaṃvarā,
- tri in tatridaṃ, tatrime & tatrimāni
- tru in citrupāhanaṃ, tatrupāyāya & tatruppattiyā
- tva in tvaṃ, tatvassa
- gya in ārogyaṃ, manussadobhagyaṃ, agyantarāyo
- sya in ālasyaṃ, anālasyaṃ
- bra in bravitūti, brahantaṃ, brahā, brahāraññaṃ, brahāvane, brahma
- dra in udrabheyyuṃ, gadrabhaṃ, dukkhudrayaṃ, dudrabhītipi, devadudrabhi, bhadraṃ, saudrayā
- vya in vyatto, havyaṃ, vyattūpasevī
- tre in lokacitresu, aññatreva, tatreva
- smi in abhibhosmi, panasmi, kasmiñci, ummattosmi, pismi, kismiṃ
- snā in asnātha
- sne in sasnehaṃ, sneho, snehapareto
- ste in anuddhastena, uddhaste
- sta in biḷārabhastaṃ, odhastapatodo
- kri in kriyavādā, kriyā
- kru in akrubbaṃ, krubbetha, vikrubbato
- pla in plavanti, uplava, uplaveyyāti, uplavissati
- dva, dvi & dve in advayaṃ, vākyadvayam, dvinnaṃ, dvidhā, dvipadā, dve, dvedhā, dveḷhakajātā
- kya in vākyam, sakya, mālukyaputto, abhinanduntivākyaṃ