GSTR turnover and 44ae

Is the GSTR3B turnover pertaining to transport activity from these 4 vehicles?

Yes fright revenue 

The reporting in GSTR3B is sales, whereas reporting under 44AE is net income or profit. So there should not be any issue in this case. 

Let's consider some business other than transport and assume there are no cash receipts at all, which means that the business will now qualify for 44AD with a limit of 3 crores. In case of such a business, for the same 2.5 Cr turnover, presumptive income will be considered at 6%, which comes to 15 lakhs income or profit.

Coming back to your case, the total turnover from transportation activity reporting in GSTR3B is 2.5 cr, and the total profit from transport activity under 44AE is 17 lakhs, which indicates a profit ratio of around 7%, which seems to be acceptable.

It is to be noted again that, the difference between GSTR3B and 44AE is that, GSTR3B reports sales and 44AE reports profit or net income.