Yes, there is an important reason to distinguish them phonologically.
Well, let me explain better. This is for a conlang that I'm creating, whose phonotactics rules are very restrictive with stop consonants. Due to this, several loanwords have to be adapted, so I had thought that, when a stop is in a forbidden position, it might be replaced for a fricative (/p/ > /f/, /b/ > /v/, /k/ or /g/ > /h/) or an affricate (/t/ > /t͡ʃ/, /d/ > /d͡ʒ/), according to the "natural" evolution of the old language. So I wanted to know if an affricate can make a cluster with r or l, for example, to adapt the word /dɾakul/ as /d͡ʒɾakul/ (stops can't start a word).
Yes, I know English R is not /ɾ/ but /ɹ/, it was just an example, I thought they could be considered equivalent in this context. In any case, my language uses /ɹ/ like English.
Thanks for help.
PD: Sorry for my mistakes, English is not my native language.