Since the vast majority of non-EU immigrants to Portugal apply under Article 88.2/89 (from Brazil, South Asia, as described earlier) and the nationality law change was for their benefit, I thought it would be instructive to compare the stages and timelines of immigration under Article 88.2/89 with ARI. They are remarkably similar. (Time periods quoted are typical, several extreme cases we’ve seen on this forum extend far beyond the typical, especially during covid)
Step 1: Application
88.2/89: Register on the SAPA portal, upload NIF, NISS, work contract etc. and get an acknowledgment. AKA Manifestação de Interesse, Expression of Interest, “file lock”. This happens pretty quickly, a few days perhaps. With the MI number, the applicant can work, pay taxes, etc.
ARI: Register on the ARI portal, upload docs, proof of investment, etc. Get acknowledgment, followed by a request to pay the analysis fee. This is also a matter of days. The investment has started contributing its mite to the economy.
Long Delay 1: We enter the long dark teatime of “analysis”. It used to be a few weeks in 2018/19 but has now stretched out to an average of about 18 months or more for both 88.2 and ARI applications.
Step 2: Application analysis is successful.
88.2: The applicant gets an “IM acceptance” email, also known as “first email from SEF” in South Asian forums.
ARI: Applicant gets the pre-approval mail, titled “ARI - Notificação de Aceitação”
Short Delay 1: usually a few weeks
Step 3: Applicant gets a notification asking them to book biometrics appointment.
88.2: AKA “second mail from SEF”
ARI: AKA “Biometrics opened”
Short Delay 2: usually a few weeks
Step 4: Biometrics
88.2: Updated documentation, evidence of job and paying taxes, etc.
ARI: Updated documentation, evidence of maintenance of investment, etc.
Long Delay 2: This could be as short as a few months but can easily take longer than a year or two, depending on where you gave biometrics. Delays are of the same order for both types of applications. More complications possible with 88.2 because of blacklisted employers, investigations, etc.
Step 5: Final approval. This is the point where you pay the fees for card issuance.
Short Delay 3: a few weeks to a few months, same for both.
Step 6: First residence card arrives.
TLDR; the ARI application lifecycle is very similar to that of Article 88.2/89. Both applications face two instances of long delays.
The text of the amended law says (official parliament proceedings): For the purposes of counting legal residence periods provided for in this law, it is considered also the time elapsed since the moment the temporary residence permit was requested, as long as it is granted.
For the vast majority of cases (i.e. 88.2), the simplest interpretation of the law should cover both long delays, and the date considered would be the date of the acknowledgment on Step 1. This is logical and just, since migrants under 88.2 are living, working and paying taxes at least from that date. For the rest - we few, we happy few - might be dragged along in their wake, with the not-quite-as-strong justification that our investment has similarly been working and paying taxes, and we have been subjected to uncertainty and delays beyond the prescribed legal limits. Or we may not 
Anyway, I think ARI cases will either be backdated to Step 1 or not at all. Not seeing the logic of backdating to Step 4 or 2.