No counts for added gene in cellranger (scRNA-seq)
The first column of your GTF must correspond exactly to the name of the sequence in your FASTA file. Typically this is the chromosome so a GTF line:

chr1    hg38_knownCanonical exon    11106535    11262507    0.000000    .   .   gene_id "gene1"; transcript_id "tx1"; 


This must have a corresponding sequence in the FASTA file:

&gt;chr1
ATCG ATCG ATCG ATCG ATCG ATCG...


Therefore you need to add an additional sequence to your FASTA file with &gt;TdTomato. This must have exactly the same sequence as the construct that you are expecting reads for. The run cellranger mkref and cellranger count on these FASTA and GTF files. Cellranger also can take a GTF with “CDS” as a feature in addition to “exons”. The STAR alignment algorithm used by cellranger is splice aware so it can handle split reads but you will need to ensure the GTF corresponds to exons of the mRNA/cDNA rather than the full sequence.

10x Genomics is a platform with a high dropout rate, especially for lowly expressed genes. You should bear this in mind for what you expect to observe. It may be worth comparing the mapping rate of your construct to housekeeper genes to see if this is the reason for the low counts. Since whole mRNA molecules are captured on the beads before preparing the library, there should not be a difference in UMI counts between long and short genes.